Itinerary - Nara, Nikko, Koyasan, or Takayama

So we are headed to Japan in May with a group of 11 adults and 1 toddler (my daughter who will be 3 yo at the time). You may have seen my previous posts about deciding between Okinawa and mainland Japan. After hearing all the ideas here and another group (thank you to everyone who replied) about this, we have decided to stick with mainland Japan only.

A little background on our group --> we tend to move around fast, we like a change of pace/scenery and would not want to do temples all day. Trying to keep it balanced between "city" and "shopping" and "temples" and "scenery" as much as possible.
We will be taking the Shinkansen whenever possible and will invest in the JR pass in advance. When we are in Kyoto, we plan to hire a private van with driver to take us around to the places we want to go to avoid walking so that we can cover more ground while we are there.

We will definitely be visiting Tokyo (3 full days and 1/2 day), Osaka (1/2 day but hope to keep this as our base when we are in the Kyoto area as I hear food and night life is better here), and Kyoto (2 full days). We still have a few days to spare and are stuck between the following destinations:

1. KOYASAN
2. NIKKO
3. NARA
4. TAKAYAMA (along with a visit to SHIRAKAWAGO)

If you could add 2 or more of these places, which one would you add? I would love to hear from people who have been to most or all of these places to give me a comparison.

Koyasan but I am not sure if it is possible with a toddler - especially staying in a Buddhist temple. My daughter is average in terms of "well-behaved"�cshe's not hyper but she's also not "quiet" and I have no idea how she will be in 5 months as their temperament continues to change like the size of their shoes.
Thanks in advance!

With your group I would look at Nara or Takayama. I would also consider Karuizawa.

Nara is one of my favorite areas in Japan and it is more spread out so that you can have a break from the crowds. Much of it is park and I try to get accomodation as close to the park as possible. It has OK but not good shopping, but it is handy to Fushimi Inara and Uji which have some interesting shops as well (Fushimi Inari gets very busy these days).

Takayama is a lot different to the other places you are going. The old town is nice, the beef is good, there are some great things to see and do there though I having found it a place to buy much interesting stuff. It is also pleasant in the early morning before it gets busy. Accomodation is pretty cheap, I really like the Hotel Associa there.

It just so happens that we will be over in April and made sure to spend a few days in each of Nara and Takayama, where we have been multiple times before.

Karuizawa is also a good option. About an hour from Tokyo by Shinkansen, a fairly trendy town by Japanese standards with nice mountain views and it is also quite a bit cooler which would be good if May is hot as it was last year. It has brilliant restaurants and fun shopping, though a lot of people go to the big outlet shopping centre there which is pretty much the same as every other outlet shopping centre anywhere, my preference is the little shops in the Gion street. It also has a section of the Nakasendo way to walk/hike leading to a great lookout. Accomodation at Le Grand Kyu is probably the best bang for the buck I have experienced in Japan.

I have been to all 4 of these destinations (the only place I haven't been to is Shirakawago).

Nara has the great advantage that it is doable as a day trip from Kyoto (or Osaka). Depending on where you are staying. I.e. it add flexibility to your schedule. E.g. bad weather and you can skip. Plus Nara has the deer, which is something special. (not everyone likes them... but have you been ever chased by semi-friendly deer?)

Nikko has the advantage of a slightly different landscape. It is doable as a day trip from Tokyo, although it involves more transport time than Nara from Kyoto/Osaka and I personally would do it as an overnight trip.

Takayama is the one place that needs most transport. And I personally didn't really like it as I thought it was overwhelmed by tourists. Although probably in comparison with Nikko and Nara, it gets less than Nara and probably around the same as Nikko.

Koyasan, needs approximately the same transportation time as Nikko but is different. The big plus of Koyasan is staying at a temple and visiting the cemetery. Now temple in 11 people and with a toddle might be challanging. I dont even know if you can find a temple lodge for so many people. And cemetery with a toddler is maybe also sub-ideal.

Thus I personally would go to Nara. Or second choice Nikko, because both are doable as daytrips, which gives you added flexibility.

Also with a group of 11 you might have people who want to visit something different that day. E.g. Himeiji , Kamakura, stay in Tokyo/Kyoto/Osaka. Which if a part does a day trip to Nikko/Nara is doable. While both Koyasan and Takayama essentially need a night.

Hope this helps.

Enjoy your trip to Japan!

Hi!

I think Takayama is fine and my child loved the Hida no Sato village but I find Shirakawa Go boring. Yes, it is scenic, but when I went it just seemed to be tons of cafes/restaurants and shopping, and not even interesting but the same touristy things in shops. I went in 2010 before it was super touristy so I can't imagine how crowded it is now. I preferred Hida no Sato which was pretty empty when we went in '17 and I regret we didn't stay longer. Yes, it's a model village vs a "living" village like Shirakawa Go, but because it's a model it shows how traditional life use to be while Shirakawa Go is made up of lots of tourist facilities so that the people who live there have a livelihood.

Takayama (and Shirakawa Go) are a pretty long trip for just a single night. I am not sure I would want to do it with a toddler. I know when my kid was 3 they wanted to be out and walking around as much as possible.

BTW this is not to put Osaka down, but how good the dinning and nightlife options are sort of depend on what you want to eat and what you want in nightlife. I do often go to Osaka because I have a friend who lives there, but until last trip, I found good restaurants for my personal dinning requirements challenging. In certain respects, I think Kyoto offer more apartment hotels or other options for larger groups vs. Osaka, so that is something to think about.

Good luck!

BTW, by the time you are hiring a minivan and tour guide to take you about, you may as well look at some of the offered day tours and see if any of them work for you.

Thank you so much all!
I have come up with the following proposals on itineraries for our group, can you please review and see if it seems ok?

Proposal 1 includes - Tokyo, Osaka, Kyoto, Nara, Takayama, Shirakawago

Day 1 - Arrive Tokyo at 2:45pm, evening in Tokyo
Day 2 - Tokyo
Day 3 - Tokyo
Day 4 - Transfer to KYOTO (4 hours)
Day 5 - KYOTO
Day 6 - KYOTO
Day 7 - Day trip to NARA + Osaka
Day 8 - Takayama + Shirakawago (3 hour 30 minute one way)
Day 9 - Takayama + Day trip to Kamikochi (45 minute bus ride)
Day 10 - Takayama in morning/afternoon, evening train back to Tokyo (4 hour 45 min)
Day 11 - Tokyo
Day 12 - Flight back to USA


Proposal 2 includes - Tokyo, Kyoto, Osaka, Nara, Nikko, Kobe, Koyasan

Day 1 - Arrive Tokyo at 2:45pm, evening in Tokyo
Day 2 - Tokyo
Day 3 - Tokyo
Day 4- Tokyo
Day 5 - Transfer to KYOTO (4 hours)
Day 6 - KYOTO
Day 7 - KYOTO
Day 8 - Nara + Osaka - spend night in Osaka
Day 9 - Day trip to Kobe
Day 10 - KOYASAN (2 hour journey one way)
Day 11 - KOYASAN in morning and evening in Tokyo
Day 12 - Flight back to USA

sorry forgot to add my edit on itinerary 2

Day 9 - Day trip to Kobe (or can replace this with Nikko earlier on in the trip at Day 5)

sorry forgot to add my edit on itinerary 2

Day 9 - Day trip to Kobe (or can replace this with Nikko earlier on in the trip at Day 5)

Hi!

Just to note, it's not only a 45 minute trip to Kamikochi from Takayama. It's 58 minutes alone from Takayama to Hirayu onsen. You then need to wait to catch a bus to Kamikochi which is another 20 to 30 minutes depending on which station you want in the Kamikochi area. None of the buses from Hirayu to Kamikochi are timed to the buses to Takayama so you will always have a 15-20 minute leftover. Kamikochi is really rewarding but it is a long day after a long day to Shirakawa Go.

BTW you might want to consider going fro Kamikochi to Matsumoto and then from Matsumoto back to Tokyo.

Also it's more like 3.5 hours by train from Kyoto to Takayama, Shirakawa Go is an additional 1 hour to Shirakawa Go, unless you are planning Kyoto to Kanazawa to Shirakawa Go which is a little more than 2 hours plus the 2 hour trip to Takayama but Shirakawa Go is about 1/2 way there.

If you really want to do Takayama and environs I would do: Kyoto to Kanazawa to Shirakawa Go to Takayama (night)
day 2 all day in Takayama
Day 3 go to Kamikochi and overnight either there or Matsumoto and then come back from Matsumoto to Shinjuku is about 3 hours. (or continue on to Nagano from Matsumoto and give yourself only a 1.5 hour trip to Tokyo your final full day in Japan)

Good luck!

rkold, thank you so much!

We would like to spend the night in the houses in Shirakawago.

Day 9 - Can we do a direct transfer from Kyoto to Shirakawago? Spend the day and evening here.
Day 10 - Takayama today, again spend the night in Shirakawago?
Day 11 - Either go to Kamikochi and then head to Tokyo or another option here somewhere? Basically need to get near the airport by night time as the first set of people in our group have a flight at 10:30am the next day.
Day 12 - Flight back to USA

Hi!

There are no direct buses from Kyoto to Shirakawa Go. If you want to go there you are probably better off going Kyoto to Kanazawa by Limited Express and taking the bus from Kanazawa. I would think that would be the fastest route.

I think getting from Shirakawa Go to Kamikochi is going to take longer than you think. You can see some of the bus fares and times here:
https://www.nouhibus.co.jp/highwaybus/kanazawa_en/

If you took the first bus from Shirakawa Go at 9:35 you get to Takayama at 10:25 You can then take the 10:40 bus to Hirayu and arrive at 11:38, you then need to wait you will have to take a noon bus and you will not get to Kamikochi until 12:30.

You are probably better off going from Kamikochi to Matsumoto to Tokyo because otherwise you need to backtrack Kamikochi to Hirayu to Takayama to Nagoya to Tokyo because if someone has a flight at 10:30 am the next morning you really want to be in Tokyo the night before. I had a 10:40 am flight from Haneda to JFK in July 2019 and I left at 8ish and just barely made my flight because there was such a long line of people checking suitcases.

Realistically you only have until 16:40 in Kamikochi before you need to catch the bus to Matsumoto to arrive by 18:30 and then try to find a train to Tokyo. There is an 18:40 that will get you into Tokyo by 21:06 (going by the current date in Hyperdia, things could change) Matsumoto is small enough that 10 minutes should be enough for the transfer assuming you already have reserved seats and just need to get on the train and you don't have too much luggage.

If you wanted to go the other route back through Takayama If you left at 16:30 you would be in Hirayu at 16:55 and have a layover until 17:30 and then would get to Takayama at 18:31, you would then take a 16:47 train from Takayama to Nagoya and if you were using a rail pass that doesn't allow Nozomi trains you would not be in Tokyo until 23:08, without a pass it would let you get in at 22:53. This route would also cost considerably more than the Matsumoto route.

Personally, you would have to pay me to spend that many hours traveling with a 3 year old before having a 10+ hour flight from Japan back to the US the next day. Heck my kid is 9 and I still would not be willing to do that much traveling the day before our flight back to the USA.

If you wanted to do Kamikochi, I would do 1 night in Shirakawa Go and 1 night in Hirayu onsen, that way you have less travel when you visit Kamikochi and you're not back tracking an hour in the wrong direction the day before.

Good luck!

And if spending two nights in Shirakawa Go is the priority then I would roundtrip back to Kanazawa, see the garden and do other touristy things there before taking a shinkansen back to Tokyo since Kanzawa is the current last station on the Hokuriku shinkansen line.

Good luck!

rkgold you are SO awesome! That all makes more sense than the internet did on it's own!!!

So here is what I am thinking keeping that in mind (if I understood you correctly):

Proposal 1 includes - Tokyo, Osaka, Kyoto, Nara, Takayama, Shirakawago
Day 1 - Arrive Tokyo at 2:45pm, evening in Tokyo (night in Tokyo)
Day 2 - Tokyo (night in Tokyo)
Day 3 - Tokyo (night in Tokyo)
Day 4 - Tokyo (night in Tokyo)
Day 5 - Transfer to KYOTO (4 hours) (night in Kyoto)
Day 6 - KYOTO (night in Kyoto)
Day 7 - KYOTO (night in Kyoto)
Day 8 - Day trip to NARA + Osaka (night in Osaka)
Day 9 - Transfer to Shirakawago via Kanazawa (direct train) - (night in Shirakawago)
Day 10 - Takayama - (night in Takayama)
Day 11 - Kamikochi in route to Tokyo w/ direct transfer bags to Tokyo) (night in Tokyo near airport)
Day 12 - Flight back to USA
ALTERNATE TO ENDING OF PROPOSAL 1:
Day 9 - Transfer to Shirakawago via Kanazawa (direct train) - (night in Shirakawago)
Day 10 - Takayama - (night in Takayama)
Day 11 - Spend day in Kanazawa (famous garden) and then head to Tokyo w/ direct transfer bags to Tokyo) (night in Tokyo near airport)
Day 12 - Flight back to USA


Proposal 2 includes - Tokyo, Kyoto, Osaka, Nara, Kobe, Koyasan
Day 1 - Arrive Tokyo at 2:45pm, evening in Tokyo (night in Tokyo)
Day 2 - Tokyo (night in Tokyo)
Day 3 - Tokyo (night in Tokyo)
Day 4- Tokyo (night in Tokyo)
Day 5 - Transfer to KYOTO (4 hours) (night in Kyoto)
Day 6 - KYOTO (night in Kyoto)
Day 7 - KYOTO (night in Kyoto)
Day 8 - Nara + Osaka (night in Osaka)
Day 9 - Day trip to Kobe (night in Osaka)
Day 10 - KOYASAN (2 hour journey one way) (night in Koyasan at a regular hotel)
Day 11 - KOYASAN in morning and transfer to Tokyo (night in Tokyo)
Day 12 - Flight back to USA

Hi!

If you're planning to go to Kanazawa and then onwards to Shirakawa Go, I would not spend the night in Osaka. Why add an extra 30 minutes onto your train ride the next morning? You save 30 or so minutes catching the train from Kyoto vs. Osaka and quite honestly I am not sure how much nightlife you will be enjoying with a 3 year old. I have no idea if you've traveled a lot with your child, but I know it takes mine a while to adjust to time changes in Japan. She did fine with NY to CA (She's been doing that distance since 2) but Japan is tough. In Japan she tends to be a morning person. It also involves another hotel move which with 11 people is going to be less than fun.

I'm not sure what you mean by luggage transfers. There are certainly luggage forwarding service, just be aware that most have rules about how far in advance bags must be sent to the airport. I want to say it is 48 hours? I remember running against it trying to get bags from Kyoto to KIX and they're not even terribly far apart. Please make sure to check on that before counting on using it.

I don't know which airport you are using, if it's Haneda, you can easily still stay in Tokyo before a 10:30 am flight. I did it. It is harder for Narita, but I don't know if you really want to do all that travel to Narita with a 3 year old unless it is your flight leaving that early. If it is someone else in your party they can just get up early. To get to Narita from Tokyo Station you just need to get to Tokyo Station by 7:27 and you are fine. Ueno gives you even a bit more leeway, Shinjuku gives you less. I know a lot of the flights from the US have been moving to Haneda vs. Narita. I've noticed it when looking at my Summer trip. If I use ANA I get Haneda and if I use JAL I get Narita.

Honestly, I would look at the sights you have listed and figure out what you want to do and what your interests are. I would also talk to the rest of my group. 11 people is a lot. If anyone in your party has dietary restrictions, make sure there are options where you are going. Japan is not always good with dietary restrictions or food allergies.

Good luck!

rkgold,

You are right about the extra 30 minutes from Osaka to Kanazawa - but for the night life it would be us leaving the toddlers with her grandmother (my mom) and my aunt who usually do not come out for the night life because they are early sleepers. We tend to do this a lot when we travel - the advantage of going in a family group of various ages lol. But definitely I would love to avoid the "one extra hotel" because that is bothersome especially with our large group. I will discuss this with my group and see whether they are ok with the extra hotel and prefer to spend the night in Osaka or vice versa. We really would like one evening in Osaka so I know that for a fact

Yes I meant luggage forwarding. Someone in TripAdvisor suggested this so that all our luggage goes to Tokyo while we are still sightseeing around kamikochi etc. It would not be to the airport.

WE are flying out from Narita - unfortunately. The good news is that my mother and father in law have the early flight at 10:30 am (the rest of us leave at 3:00pm) so I can send them on their way if they are comfortable getting there on their own - or pay for a private transfer for them. My husband and myself are usually the leaders of the group getting everyone around.

The group likes both itineraries and ultimately they will have me select. No food allergies. Only restriction is vegetarian for half the group.

Hi!

Yeah, I was wondering if anyone in your party was vegetarian because depending on how strict they are being vegetarian in Japan can be challenging. My family is vegetarian. I think you should make sure staying overnight in Shirakawa Go your family group will actually be able to eat the food. I have not looked recently, and I know things are changing, but when I did look in 2010, vegetarian was not an option. I would also make sure if it is an issue that the website you use to book understands if members of your group don't eat traditional fish broth either. I don't eat dashi (traditional broth) and it is one of the reasons I don't use JapaneseGuestHouses to book reservations since they only have the option for vegetarian with fish broth (which is not vegetarian to me.. just like vegetarian but eats fish isn't vegetarian, you're a pescatarian, own it, but I digress) You will also need to check for Koya-san since some places just do vegetarian style not actually vegetarian. Be aware that some places are super easy to be vegetarian (Tokyo) and others can be much harder. If members of your party don't eat eggs either, look into that now, hungry people make for cranky travel companions.

The good news is a lot more places are offering vegetarian options. I was positively shocked by how many ryokan in the Yudanaka/Shibu onsen area offer vegetarian options.

I guess I am just not a nightlife person. I've stayed out as late at 22:00 in Osaka and still returned to Kyoto to sleep. We were staying right near Kyoto Station so it wasn't a big deal, but I could have easily made it back to anywhere accessibly by subway without too much difficulty.

May I ask why you want to stay overnight in Osaka? I am not trying to put Osaka down, I have gone there many trips, but make sure you know why you want to stay there, since you have limited time and every time you change hotels you will need to forward bags or find somewhere to store things for the day or both. It's an added expense both in time and in money. Last time I needed to store two carry-on size bags in Osaka Station ,I had a miserable time and ended up just paying more for Sagawa to get it done. I can tell you that your vegetarian members of the party are not going to be as thrilled with food options in Osaka unless they are actually pescatarian, Osaka is known for food, but it's mostly seafood or pork related foods.

The forwarding service is great but you will need to send bags a good 48 hours before your flight is supposed to leave so you need to send bags on day 9 or 10 if you want them to go to the airport and will need to check if day 10 is too late for the people leaving at 10:30 am. You can send the bags to your Tokyo hotel, but you still need to send them the morning of day 10 so they can hopefully arrive by the 11th, you can't send anything the 11th and hope to have it on time for your flights on the 12th. Kamikochi does have lockers but they can get full. It was pouring buckets of rain when I went to Kamikochi so finding a locker was a non-issue, but we also rented a cabin and stayed overnight.

I would still probably stay in Tokyo even if you're using Narita, you'll do better finding dinning options outside the airport itself and catching a 7:00-7:30 train is definitely doable, just make sure to spend that night close to Ueno Station so you can take Keisi or Tokyo Station if you plan to use JR. If you're using JR from Tokyo Station to get to the airport it's pretty straightforward, you just follow the English signs for the NEX and get on the NEX. It goes directly to the airport and usually has no stops to let people off until you get to Narita. The Keisi is the private line and should be equally straightforward from Keisi Ueno Station. You just take the Skyliner until the terminal you need. I believe both are reserve seats which makes the whole thing easier. I've mostly used JR in the past, but might use Keisi in February, depends on if we eat in the airport before we head to Tokyo.

Good luck!

Thank you for all your detailed notes.
JapaneseGuestHouses - I looked at the house food options in Shirakawago and went to "book" it and it gives me the option to have vegetarian food without fish broth. I just confirmed with the vegetarians in my group nevertheless and if absolutely necessary they are ok with fish broth but of course would prefer not to because I am sure the taste can be strong. This was such a good suggestion to look into which places have veggie options and base our decision on that because we don't want any HANGRY travelers!!

22:00 in Osaka is perfect, we won't be out all night either. I am sure we will be tired. So I think this might be a better idea then to just go back to Kyoto. Just not sure what I will do with the moms and toddler. Will need to figure something out about them because they won't be comfortable traveling alone and I definitely don't want them taking my toddler on public transportation without me or my hubby. So we will then just stay in Kyoto in that case. Unless we go with Itinerary two, then we may stay in Osaka because it is two nights.
Good to know about the forwarding service being slow. I honestly thought it would get to the station the same day. Did not think it would take more than that so I guess I can't do that option. This is giving me more things to think about.

Hi!

It's actually not that slow when it comes down to it, I've not seen anything close to it in the US. It just takes 24 hours unless you are in certain limited same day locations. You're looking at Takayama to Tokyo, that's really far! It would take you over 4 hours if you were to go direct and cars do not go as fast as shinkansen. Most luggage forwarding needs approx ~24 hours. I would personally want to give myself some extra wiggle room if you are going to be leaving early the next morning. I've never had a package get delayed yet, but that certainly doesn't mean it couldn't be. I have had trains get very delayed.

Depending on where you are staying in Kyoto getting between Osaka and Kyoto is quite easy. Honestly, if you're not comfortable with them traveling alone, post Nara, just go back to Kyoto and then go down to Osaka. It is a longer trip, but it's probably less time than you would have spent taking bags from Kyoto to Nara finding lockers or storage and then taking bags from Nara to Osaka to your hotel, settling people in and then going back out again. Just pick a smart location in Kyoto. I don't know your price and if you all want to share one or multiple rooms, but there are lots of options in Kyoto in convenient locations. Just pick somewhere a short walk from a subway or train station and think about where you want to go.

If you left Nara at 17:00, you could be in Kyoto by 18:00 and in Osaka by 19:00, giving you 3 hours to explore nightlife, heck you could even plan to go to Osaka every single night you are in Kyoto. It's a cheap, easy and frequent trip. JR Kyoto Station has Special Rapids to Osaka every 15-20 minutes. If you're closer to the Hankyuu line, use that. Just remember, there are lots of non-JR lines in places like Kyoto, Osaka and Nara. when I was staying near the Keihan line, I took that to Osaka.

And i guess now is the time to bring up whether a JR Pass makes sense or not. Depending on where you go and the route you take a JR Pass might just barely break even or might not break even. The plus of not having a pass is you can use the fast Nozomi shinkansen which are faster and run more often.

Please be aware that starting in May larger luggage will not be allowed on some shinkansen, including the one to Kyoto without a reservation
https://matcha-jp.com/en/7887?type=news

Good luck!

I am bumping this thread up because of some changes that we have made to our itinerary and looking for suggestions....after much of your help in this thread and thinking about the logistics of traveling with luggage and a toddler...we thought about the idea of spending the last few days in Kyoto and doing day trips instead - allowing us to stay in the same place so we are not lugging things around except for what we may need for the day.

Please throw in your thoughts on the following:

Day 1 - Arrive Tokyo at 2:45pm, evening in Tokyo (night in Tokyo)
Day 2, - Tokyo (night in Tokyo)
Day 3, - Tokyo (night in Tokyo)
Day 4 - Tokyo (night in Tokyo)
Day 5- Transfer to KYOTO (2.5 hours) + NARA afternoon trip with a guide we already booked (night in Kyoto)
Day 6 - Day trip to Osaka (night in Kyoto)
Day 7 - KYOTO (night in Kyoto) - booked a photoguide to take us around
Day 8 - Day trip to Kanazawa + Shirakawago (night in Kyoto) EARLY MORNING (2 hours each way from Kyoto to Kanazawa, and then 1 hour bus ride from Kanazawa to Shirakawago). Alternatively we can go to Gokayama instead of Shirakawago. Alternatively we can go to Takayama and just visit the museum there and skip all the others all together?
Day 9 - KYOTO (night in Kyoto) - booked with a photoguide to take us around
Day 10 - Day trip to Hiroshima + Miyajima Island (night in Kyoto) (1 hour 15 minutes each way) (night in Kyoto)
Day 11 - KYOTO in morning (planning to hire a van to take us to some further sites like Kifune shrine etc) and transfer to Tokyo via shinkansen later in the day (night in Tokyo)
Day 12 - Flight back to USA

Hi, while you would reach both cities your time doesnt permit you doing anything there, personally I think it is a waste of a day.

Also I dont really see the point in daytripping from pretty much the most expensive place to stay, the miser in me suggests that if I am paying to be in Kyoto I should stay in Kyoto and immediate surrounds.

I would kill your half day in Nara as it isnt enough, and use the other day for a full day in Nara which also isnt enough, but is better than a half day.

Hi VPPATEL,

I think you are smart to limit the number of hotel changes. I think with a larger group it gets hard to keep changing hotels and you are traveling with a young child, so I think staying in one place for more nights makes sense.

Are you planning to use a JR Pass and have you made sure to not include Nozomi in your time estimates?

In the case of the trip to Hiroshima from Kyoto it is anywhere from 111 minutes to over 130 minutes. It and Miyajima are totally possible as a day trip from Kyoto. (I've done it multiple times) but be prepared for a longer trip than just 1 hour and 15 minutes each way.

I think going to Kanazawa from Kyoto is a do-able day trip (I've done it) but I think Shirakawa Go or Takayama is getting a little longer. It is only about an hour from Shirakawa Go to Kanazawa, but the buses are not necessarily timed for the trains and so you might spend more time waiting in either direction. It's more like 2 hours just by bus to Takayama from Kanazawar you could go Kyoto to Nagoya to Takayama and with good time it might be a little faster. I just want to throw out there, the last time I took a limited express train from Nagoyaa to Takayama (and then Takayama to Toyama) no snacks were sold on the train and all the toilets were squat only. I am not sure you want to do a squat toilet on a moving train with a 3 year old.

Kanazawa has a lovely garden and lots of other interesting sights including an art museum, the castle, some shrines and temples. and a merchant quarter.

Good luck!