3 Week Itinerary Advice

Hi everyone,

I'm heading to Japan for the first time ever towards the end of this year 26th Dec to 16th Jan) and will be travelling alone. I know I really wanted to see snow and was thinking of travelling to Nikko and Nagano for the first few days before looping back to Tokyo for New Years Eve and then exploring the rest of southern Japan from there (I originally planned to head to Sapporo via train after I landed but don't think the trek was worth it) I'm not too sure if this is the most effective way of exploring the country and I just wanted some advice or suggestions for this itinerary outline I made:
(I have a few things in mind in regard to what I want to do in each other cities at the moment, but I'm very open to alternatives and any must do/see activities!)

26th Dec
- Arrive at Narita (6am), explore a bit before heading to Nikko

27th Dec
- Full day in Nikko

28th Dec
- Nikko to Nagano

29th Dec
- Full day in Nagano (I wanted to see the snow monkeys)

30th Dec
- Nagano to Tokyo

31st Dec to 2nd Jan
- Full days in Tokyo (I definitely want to explore Odaiba) and maybe catch the Emperor's Greeting on the 2nd

3rd Jan to 6th Jan
- Tokyo to Osaka
- Have a day trip to Nara on the 6th

7th Jan to 10th Jan
- Osaka to Kyoto

11th Jan
- Kyoto to Hiroshima
- Head to Miyajima to stay overnight

12th Jan
- Miyajima to Nagasaki (stay overnight)

13th Jan
- Full day in Nagasaki (stay overnight)

14th Jan
- Nagasaki to Tokyo

15th Jan
- Tokyo to Narita

16th Jan
- Flight back home to Sydney (10:45AM)

The one thing that really sticks out is your plan for going back to Tokyo from Nagasaki in one shot. I hope to God you are planning to fly - if you used a rail pass it would take you over 8½ hours and with the faster Nozomi train, about 7 hours. Either way, it's completely murdering the day. You could take a low cost carrier like Jet Star for at little as 4500 yen to Narita, or there is ANA's Experience Japan Fare for 10,800 yen to Haneda.
http://www.jetstar.com/jp/en/home
http://ana.ms/20Xtf8t
For your arrival day, you may not be crossing a lot of time zones, but I wouldn't expect too much on your first day - you will still likely arrive dead tired and not ready to start storming the tourist sights. And regarding your plans in Tokyo, you should definitely check where you plan to go carefully - many places will be closed at the end/start of the year. Typically shrines and temples are open, so go see those when other places are closed.
There is also little need to spend 3 days in Osaka if you are already seeing Tokyo. Everywhere has something of course, but Osaka really comes alive at night and you can easily go see the city after a day of sightseeing in Kyoto. For your daytime hours, you could certainly go and see Himeji for a day. The castle is the finest original surviving castle in the country, and the Kokoen Garden near it is exquisite.
https://goo.gl/65ZtRi
Get the combo ticket for both and one is virtually free. You could also spend a day in Kobe if you like, and in Shiga, there is also Hikone Castle which is also a very nice original.
https://youtu.be/dCp5HCc6rYQ
On Jan 11-12, you don't give times of travel, but I hope you give both Hiroshima & Miyajima the time they deserve. In Hiroshima City, there are so many people who just see the Peace Park/Museum and then leave. There is so much more to the city than that - the Shukkeien Garden is really nice, and the secret gem of the city is the Mitakidera Temple, which is as breathtaking as it is uncrowded.
https://goo.gl/fAz4ax

For Jan 15, you might consider going to Narita early and seeing some sights there.
https://www.japan-guide.com/e/e6400.html
If you want a cheap way from/to Narita, there is the 1000 yen bus.
http://accessnarita.jp/en/home/

With a 3 wk vacation, one thing you do have is lots of time (but not enough to see the whole country). So spending almost a whole day on train for Nagasaki-Tokyo is not a big waste. I took trains from Tokyo to Kagoshima in one day when I spent 4 wk in Japan. Or you can change the sequence and visit Osaka after Nagasaki to break up that trip. With 3 wk, I think you have time to visit more places, which you can plan as day-trips from places you are staying. You can remain flexible and work out the details later. You can also utilize a 3 wk JR Pass. Dec 31 to Jan 3 is a special period in Japan, and many stores will be closed so you may not be able to do/see everything you plan.
https://www.japan-guide.com/e/e2276.html

I agree with previous posters that there is no reason to stay in Osaka and Kyoto. If you do want to split it up because you just want to stay in a larger variety of places, it would make more sense to do Tokyo to Kyoto then move to Osaka and then stay in Osaka and go to Miyajima. The reason being there are few Hikaris that go all the way from Kyoto to Hiroshima vs. all Sakuras from Shin-Osaka go to Hiroshima.

I would also personally fly if I was going to do Nagasaki back to Tokyo. I've spent over 3 weeks in Japan once, but I still didn't want to spend 7-8 hours on trains in a single day.

I also agree with previous posters to check to see what will be open in Tokyo on 12/31-1/3 Shrines and Temples tend to be open and shopping areas/restaurants/cafes immediately surrounding those sights will be open, but a lot of things in other areas will be closed. I was in Tokyo Dec '05-Jan '06 and I remember even chains like Excelsior Cafe and combinis were closed for several days near my hotel. Though there are some great lucky sales bags in the shops around Meiji Jingu which was crowded and one of the only areas with lots of open places to eat.

I really like Zenkoji in Nagano. The main shopping street leading up to it had some nice cafes and restaurants. I stayed at the Metropoitan which was great because it's attached to Nagano Station. I thought the rooms were quite pleasant.

Good luck!

The nagasaki to tokyo can be used as a rest day. So no good at the end of the itinerary.

So go to Nagasaki after Tokyo, then work you way back to Tojyo through Miyajima, Osaka and Kyoto.

But if it was me. You have two locations planned between Tokyo and Nagasaki.

So...

Tokyo kanasi nagasaki miyajima tokyo. Etc

Oh wow, thank you so much for all the feedback! Appreciate it heaps and they were really insightful and very informative so thank you so much guys! I'll definitely reconsider and readjust my itinerary around a bit so that I can see more and as to not waste time throughout the trip (especially that trip from Nagasaki to Tokyo).

Looking forward to it and I can't wait to visit Japan for the first time ever, hopefully it'll be good!

Well, for a three week travel it would make sense to go for a 21 day Japan Rail Pass https://goo.gl/GPF2LP which I think its the most economic way of transport.

First obvious point - are you landing at Narita? The flights arriving into Tokyo at 6 am are usually Haneda (Tokyo International) - check your ticket. (I know because I meet them often enough and it makes for a very early start to my day - Haneda, not Narita.)
Second obvious point - your travel out of Tokyo on the 3rd is a very busy travel day - you might be lucky and be able to reserve a seat, but failing that standing to Osaka is only a few hours.
Third, less time in Osaka, more somewhere else. Three weeks you can see and do a lot, but even with much longer trips you might only be scratching the surface.

Yeah I'll definitely be getting a rail pass! Just tossing up between ordinary and green at the moment, but after looking into it will probably stick with ordinary because the extra cost doesn't really seem worth it.

@JapanCustomTours: Had me worried for a second, but just double checked and definitely will be landing in Narita on the day at 6am. Yeah I'm going to try my luck with the trains leaving Tokyo that day, but I'm currently trying to rearrange my itinerary around so that I'm not wasting my last days in Japan on the train from Nagasaki back to Tokyo.

I'm thinking on cutting back on the time spent in Osaka at the moment too as everyone keeps suggesting it. Are there any other worthwhile places that you would recommend to spend that extra time on instead?

The early Narita flights are not the usual ones that I meet as many of them have east-Asia departure points - but yes it pays to check. I've had people surprised before because they think they are landing somewhere else - often they simply think "Tokyo". So we check flight numbers for everyone to make sure we know where they are arriving.