Itinerary for 3 weeks in Japan

Dear Members,

We are very excited to go for our honeymoon to Japan this upcoming May for 3 weeks. We start in Tokyo where we land and have already booked a place for 7 nights. After that (or maybe already suing 2-3 last days in Tokyo to see nearby area for day trips?) we would like to travel by train/bus using 1 week JR pass and finish in Kyoto where we would like to stay for 6-7 nights and from there go to Osaka for final 2 days and our departure from Osaka. To break it down for more visual itinerary:
1-7 days TOKYO (and maybe its area with 1 week JR pass)
7-14 days travel in Japan by train using 1 week JR pass and see as much as possible (but not going crazy)
14-19/20 Kyoto and its area
19-21- Osaka and flight back from there.

We were thinking to get 2 week JR pass to be as flexible as it is possible but maybe it is not necessary as there are many places around Kyoto where you can travel using local transport?
We would definitely like to include Mt Fuji, Takayama, Nara, maybe Jigokudani Monkey Park and Nagano and are open to other destinations.
If anyone has any tips or suggestions we would be very thankful if you share your experience and knowledge with us.

Warmest Regards
Andrew and Anjalika from India

I've never done the JR pass so I can't answer that question, but here's another example of a three-week trip:
http://www.japan-guide.com/forum/quereadisplay.html?0+155741

And this website has a suggested itinerary which you can adapt to spend more time to Kyoto and Tokyo, and maybe an extra day in Kanazawa: http://www.japan-guide.com/e/e2400_best.html

Hope this helps!

Check out the rail pass pages on this site and find out how to work the hyperdia website to check what your costs will be - that will tell you whether it's worth getting any rail pass, or a 7 day, or a 14 day pass. It's also really useful to tell you how long it takes to get from place to place and how often the trains go.
10 mins research and half an hour on hyperdia will take you a long way.
Good luck with your planning

If you have a JR pass, you can expand your itinerary to places such as Hiroshima/Miyajima, Kyushu. These places are doable with an extra 7 days. If all the places you are planning to go to are between Tokyo and Osaka, the 7 day JR pass may not pay off.

Please keep in mind that the nationwide JR Pass makes sense/saves you money only if you make long-distance (inter-city) travel on JR Shinkansen. So if you travel only in/around Tokyo during the first week, you don't need a JR Pass for that period.

A JR Pass is for long-distance travel. If you are not traveling long distances, it doesn't save you money, so don't use for the time you are in Tokyo and around the Kyoto area. If you travel just outside of the cities, think about using regional passes instead; you can find a full list on this website.