Would appreciate comments on our Japan itinerary

We are Swiss couple planning to do our honeymoon (18 days/17 nights) in Japan. We are into the beauty of nature, old towns, and animals, but we also like cultural sights and do not want to miss vibrant cities. We have never been Japan before. It's not that I haven't done any online research to put together an interesting trip, but when it comes to traveling, experience is worth a lot. So if you have been to any of these beautiful places, I would like to ask you kindly to share your opinion with us. Is the time frame reasonable? (it shouldn't be too hectic, we do not want to rush from one point to another..) Shall we spend more time at some of these places? Are some nice spots missing which are near to these? By the way, we are planning to buy a 14-day JR Pass. Any experiences with these connections? We are thankful for any comment!

Day 1-6 = Tokyo (including a day-trip to Nikko)
Day 6 -> from Tokyo via Kamakura to Hakone
Day 6-8 = Hakone
Day 8 -> from Hakone to Yamanouchi
Day 8-10 = Yamanouchi
Day 10 -> from Yamanouchi via Matsumoto to Tsumago
Day 10-12 = Tsumago (including a walk to Magome)
Day 12 -> from Tsumago to Kyoto
Day 12-18 = Kyoto (including a day-trip to Nara/Osaka)

Hi,I'm SA-Tokyo who is Japanese office worker , living and working in Tokyo.

Have you already checked this page ?
http://www.japan-guide.com/

And when will you visit Japan ?

I don't recommend July to September.
Summer season is not suitable for sightseeing.
Tooooo hot and humid.

Anway , please ask Whatever you want to know.
I don't have enough good English skill to explain what I want to say , but I'm Japanese !
I must help your honeymoon trip.

How about KABUKI in Ginza ?
http://www.kabuki-bito.jp/eng/contents/theatre/kabukiza.html

SA-Tokyo

I'd perhaps spend a day or 2 less in Tokyo and Kyoto and try to get down to Fukouka for a few days; from there you can visit Hiroshima which I think is a must see while you are in Japan, and Nagasaki which is also accessible from there. I'd also allow a day each for Nara and Osaka, especially if you are a foodie because Osaka has some of the best food in the country.

I agree that Japan guide.com is an excellent resource - I used it a lot in my planning for my last trip to Japan.

I recommend these museums.

Edo-Tokyo Museum
http://www.edo-tokyo-museum.or.jp/english/

Fukagawa Edo Museum
http://www.kcf.or.jp/fukagawa/english.html

If you will visit Kyoto , you don't have to visit TOKYO NATIONAL MUSEUM.
http://www.tnm.jp/?lang=en

Cheers ,

If you're in Hakone (there's a three-day pass from Tokyo which covers all transport to, from and in the area) then Kawaguchiko is worth visiting for Mt Fuji and there are some excellent hikes around there, especially around the lake and up to the top of Mt Tenjo.

Similarly if you do go to Hiroshima as suggested above (the Peace Park and the A-dome are a must) then a train out to the island of Miyajima is a good day trip - wander about the small town centre of Miyajimacho along with the deer, visit Itsukushima shrine and then climb to the top of the island at Mt Misen with the monkeys (and if you feel lazy you can catch a lift on the cable car).

We were there late June/early July 2012 and that seemed like a perfect time to visit.

Enjoy Japan!

Wow thanks for all the comments, thats fantastic and very helpful! We definitely check out all these places in the further planning and already looking forward to the next comments. By the way we are flying to Tokyo (Narita) on September 20 and leaving Osaka on October 8. Is Narita worth a stay or just for transients? Thanks again!

About HAKONE
http://www.hakonenavi.jp/english/

Narita is just for transients , I think.
You had better move to Tokyo as soon as arrival.
Arriving on 20th september is good because of saturday.
Weekday morning , you can see incredible crowded trains

Cheers ,

About SUMO
http://www.sumo.or.jp/en/index

Men usually like "SUMO" , I think.
But it's time to see GRAND SUMO TOURNAMENT , from 14th sep to 24th sep ,when you stay Tokyo.
Price of tickets are from 3,800yen to 38,000yen per person.
So if you are interested in it , you can buy tickets from 8th August.

TOKYO SKYTREE Observation Deck.
http://www.tokyo-skytree.jp/en/index.html

If you like high places , try to go up TOKYO SKYTREE.
You may know birds feeling.
But this tower is still new , so you had better buy tickets by online before visiting Japan.
They sell tickets two months before your visiting.
Everyone doesn't like make long line to go up SKYTREE , don't they ?