itinerary help for honeymoon in japan?

I am going on a honeymoon to Japan from 11/11 to 11/28. I made a rough itinerary (most of it comes from: http://www.japan-guide.com/e/e2400_tokyo_19.html) and am hoping to refine it.

Here's what we have so far:

Arrival: Haneda, 9 PM, 11/11
11/11 Tokyo
11/12 Tokyo
11/13 Tokyo (Nikko)
11/14 Tokyo (Fuji Five Lakes?)
11/15 Nagoya (Ise en route?)
11/16 Takayama
11/17 Kanazawa
11/18 Kyoto
11/19 Kyoto
11/20 Kyoto (Nara)
11/21 Osaka
11/22 Osaka (Mount Koya)
11/23 Fukuoka (Sumo Basho) (Tori no ichi)
11/24 Hiroshima/Miyajima
11/25 Himeji
11/26
11/27 Hakone/Izu (Ryokan stay?)
11/28 Tokyo (Design Festa?)
Departure: Narita, 4:30 PM, 11/28

I left one day blank so that there is some time to play around with during the planning.

Here are some specific questions about the itinerary:
Is there too much travel? We don't want to stress about travel too much, especially as we'll have our luggage (we hope to pack light, but we can't pack that light. We want to be able to enjoy a place and not feel like we're racing around, though we're okay sometimes rushing. We're planning to get JR passes.

Should we move Tokyo to the back end of our trip, considering weather and koyo?

Where should we go for onsen in mid-late November? Arima? Beppu?

To give you a sense of who we are and what we're looking for in our trip:
We live in New York City. We're in our 30s. Neither of us has been to Japan before. We're looking to visit cities and also spend time in nature and at cultural sites. We are fine doing a lot of walking. We're interested in seeing architecture and design, eating local specialty dishes (though I'm the only one who eats sushi), and also going to interesting shops.

Thanks for any help.

Fukuoka stands out as being very far from the other places you want to see. I'd cut Fukuoka if that's the only place you're going to in Kyushu; it will save you a lot of time and money. Give Hiroshima and Miyajima a full day each instead.

Your itinerary looks good overall (a bit busy on some segments, but you guys are young). Since you have one open day, I would consider additional night in Fukuoka or Hiroshima/Miyajima. Since you are getting a JRPass, it doesn't cost extra to go to Fukuoka. Go see sumo.

One option you may want to consider is to move one day in Kanazawa as a day trip from Tokyo. Trip from Tokyo to Kanazawa is only 2.5 hours, thanks to Shinkansen. Then you can have more time in Hiroshima and Hakata.

Have you already booked the accommodations? If not, I am afraid you will encounter difficulty in Kyoto and Osaka. In general Saturdays tend to be busy even in non-touristic places (actually, there are no non-touristic places in your itinerary).

If you can not find good hotels in Osaka and Kyoto, see Nagoya. If you stay around JR Nagoya station, you can go to Kyoto in less than 40 min using relatively comfortable Shinkansen trains (Hikari and Kodama, not Nozomi). Fukuyama might be good substitute for Hiroshima. If you want to see Sumo in Fukuoka, you can even "commute" from Fukuyama, if you can't find good hotels in Fukuoka and Hiroshima.

If you care about packing, how about to make a group of three night stays?

Tokyo
Tokyo(Fuji Five Lakes)
Tokyo(Nikko)
Kanazawa
Takayama
Nagoya
Osaka
Osaka(Himeji)
Osaka(Mount Koya)
Hiroshima
Hiroshima(Fukuoka)
Hiroshima(Miyajima)
Kyoto
Kyoto(Nara)
Kyoto
Tokyo
Tokyo(Hakone)
Tokyo

I moved one Tokyo day to the end, based on
http://www.japan-guide.com/e/e2014_where.html

Arima could be done as one Osaka night carrying a day pack. For Beppu, you would need to drop one Tokyo day. Kawaguchiko in Fuji Five Lakes, Hakone or Izu also offers onsen. They are kinds of Arima in Tokyo.

Ise could be done en route to Osaka from Nagoya, but using Kintetsu.

The above example assumes frequent uses of Shinkansen trains. A Japan Rail Pass (14 days) should be utilized from the Nikko day to the Kyoto-Tokyo day.

Tokyo-Utsunomiya-Tokyo: Tohoku Shinkansen
Tokyo-Kanazawa: Hokuriku Shinkansen
Kanazawa-Toyama: Hokuriku Shinkansen
Nagoya-Shin Osaka: Tokaido Shinkansen
Shin Osaka-Himeji-Shin Osaka: Sanyo Shinkansen
Shin Oska-Hiroshima: Sanyo Shinkansen
Hiroshima-Fukuoka-Hiroshima: Sanyo Shinkansen
Hiroshima-Kyoto: Sanyo/Tokaido Shinkansen
Kyoto-Tokyo: Tokaido Shinkansen

I don't think your itinerary is too packed. You have a lot of days.

If you are worried about moving from hotel to hotel too much, consider staying in Kyoto for your Kyoto-Osaka portion, as a trip between the two cities is only half an hour by shinkansen.

Also, if you are staying at hotels, the staff will help you with luggage forwarding service. You can send your luggage ahead to the next hotel and travel hands free.

I agree with everyone who has said to give 2 days to Hiroshima/Miyajima.

Arima, Miyajima, and Hakone can all be onsen choices. In Arima, you can find ryokans that will serve you kobe beef. Miyajima is known for deers roaming near the hotels in the evening. And Hakone may give you sight of Mount Fuji (it is also at the end of your itinerary which means you will get the full benefits of relaxing at an onsen after a long trip).

If you mean you are going this November, then please look into booking onsens NOW. You might be too late for some of the more popular ones, especially in Hakone, and especially because you are traveling during leaf season.

I would like to offer an alternative view point to other posters (and the idea behind Japan Guide's itinerary).
While you will see many great places on your trip as it stands, I wonder how many you will appreciate in such short stays in each place.
I don't think that Tokyo, the largest city on the planet, can be fully appreciated if you don't spend at least 4 or 5 days there, at least.
Your day trips from Tokyo are all great but if you go to Nikko for a day don't try to do it all. I don't think you can fully see Chuzenjiko in one day let alone the temple area too.
I'd love to go to Takayama and Kanazawa but I don't know why you'd do both when you've only got two days for them. Why not do one properly?
I'm not sure why you would do Osaka and Tokyo as they are both big cities. I've been to both and they're great but more days in one might be better.
The reason people visit Koyasan is mostly not to look round on a day trip but to stay in a temple and observe the morning ceremonies that you will only see by staying in a temple. That's the experience that makes the place a special place to go. It was certainly a highlight for me.
I've not been to Fukuoka but I'm not sure it's worth going all that way just for it.
Hiroshima just needs two days. (Google Mitaki dera)
It might be possible to appreciate Kyoto in two days, but get there in the evening, spend two full days seeing it and you might just manage it. Three days would be better.
Going to Ise Shima from Tokyo would be a half day in Ise Shima. This is probably fine but you will only have part of the evening in Nagoya.
Sorry to be so negative about your plans. If brief visits to lots of different places is what you like to do then fine. I know people who have done similar things and said they didn't like Japan. I think that's because they didn't really see Japan because they crammed too much in. I wouldn't want you to go back home having seen a bit of how great each part of Japan is and regret that you didn't experience any one place properly.
You've planned a lot of time on trains. It'll be a tiring honeymoon.
You might need another vacation when you get back home!
Regards, Richard

Thanks to everybody for the suggestions and advice. I found so many of the ideas helpful. RichardS81, your questions and concerns forced me to rethink my approach in a way that will make for a better, more relaxing and enriching honeymoon.

I took another stab at the itinerary, taking into account everybody's guidance:

Arrival: Haneda, 9 PM, 11/11
11/11 Tokyo (just eat/sleep)
11/12 Tokyo
11/13 Tokyo (Nikko)
11/14 Tokyo
11/15 Kanazawa
11/16 Shirakawa-go (in gassho-zukuri)
11/17 Kanazawa
11/18 Kyoto
11/19 Kyoto
11/20 Kyoto (Nara)
11/21 Mount Koya
11/22 Kyoto (go straight to Osaka from Koya, then night in Kyoto)
11/23 Hiroshima/Miyajima
11/24 Hiroshima/Miyajima (Fukuoka?)
11/25 Izu (Ryokan)
11/26 Izu (Ryokan)
11/27 Tokyo (Iwatsuki in Saitama? - I know people there)
11/28 Tokyo
Departure: Narita, 4:30 PM, 11/28

What do you all think?

I streamlined the trip to reduce travel time and allow for more time to soak up the various places.

I understand that booking hotels this close to the trip may be difficult, especially at certain places, but I believe we will be able to find something or make any adjustments that are necessary.

Here are some of the day trips that I left out of the itinerary despite my interest in them: Ise, Fuji Five Lakes, Arashiyama, Kamakura, Yamanouchi, Kiso Valley

Does anybody recommend any of these to replace something else on the itinerary?

Thanks again!

Arashiyama shouldn't be a full-day day trip. It's just on the outskirt of Kyoto, so you really should be able to tack it onto Ryoanji and Kinkakuji if you're already planning to see those temples.

You can pin your interests onto a google map to help you get an idea of what's in one area and to prioritize your spots. Then you can add or subtract on the day of, depending on how you're doing on time and health.

I would drop Nikko. Koyo is basically over there. Moreover, two days would be ideal to cover Nikko (historical) and Oku-Nikko (nature), something like Hiroshima and Miyajima.

The timing favors the south and the west. Kawagichiko and Kanazawa are OK for Koyo. Takayama should be out, as you do. Shirakawago might have a chance of snow.

The following is my note for a fast-paced case to illustrate available choices. Two times slower should be much better.

11/11 Haneda, capsule hotel there. http://first-cabin.jp/
11/12 Limousine to Kawaguchiko. http://bus-en.fujikyu.co.jp/highway/detail/id/4/#routemap
Momiji tunnel. http://www.fujisan.ne.jp/event/info.php?if_id=680&ca_id=3
Mt Fuji and lake view onsen. http://www.ubuya.co.jp/
11/13 Bus to Mishima. http://bus-en.fujikyu.co.jp/highway/detail/id/29/#routemap
Shinkansen to Nagoya, Nagoya castle and local cuisine.
11/14 Ise
11/15 Namba, Osaka
11/16 Nara, night ferry to Beppu from Osaka. http://www.ferry-sunflower.co.jp/en/index.html
11/17 Beppu, ocean view onsen. http://www.seikai.co.jp/english/index.html
11/18 Fukuoka and Sumo
11/19 Miyajima, walk up to Mount Misen, Miyajima Seaside Hotel. No. 5 in http://find-travel.jp/article/1446
11/20 AM: Hiroshima Peace Park, PM: Himeji castle, night at Kobe. http://plus.feel-kobe.jp/
11/21 Umeda. Kuchu Teien. http://www.kuchu-teien.com/observatory/
11/22 Kyoto: Arashiyama, Kinkakuji
11/23 Kyoto: Fushimi Inari, Kiyomizudera, night at Gion
11/24 Kanazawa, pm: city walk
11/25 Kanazawa, am: Kenrokuen. pm: to Shirakawago, expecting the first snow there
11/26 Bus to Toyama, Shinkansen to Tokyo, Tokyo City View. http://www.roppongihills.com/tcv/en/index.html
11/27 Asakusa, Odaiba, Ginza
11/28 Shinjuku or Shibuya, to NRT

or

11/11 Yokohama. a wider room... http://www.minatomirai21.com/
11/12 Izu, Mt Fuji and ocean view onsen. http://www.fugakugunjo.jp/
11/14 Mount Koya

Iwatsuki is famous for dolls. http://www.doll.or.jp/