3 week itinerary: Where to stay?

My boyfriend and I are both first time travellers to Japan. We have organised a 7 week Asia trip in Dec. We will be starting in Japan where we are going to be spending 3 weeks (6 Dec - 27 Dec).

So far I have booked accommodation in Tokyo for the first and last 4 days (8 days). We were thinking it was a good idea to base ourselves in Tokyo and make day trips to various places.

I was thinking that we would spend 10 days in Kyoto and make day trips to various places, such as Osaka, Narra etc. I was then planning on staying in Hiroshima for 2 nights before heading back to Tokyo.

Is it a wise idea to make Kyoto a base? Are there other places that are worthwhile spending a night or 2 in. Also is there enough to do in and around Hiroshima for 3 days? There are so many places to go to and see in Japan that I find myself becoming quite overwhelmed! Any advice would be much appreciated!!!

We will be getting a 21 day JR railway pass so travel cost is not an issue.

Your plan looks ok especially for slow-pace travellers.

This is an example of what you can do for 21days in Japan.
http://www.japan-guide.com/e/e2400_tokyo_19.html