I have a similar set of priorities that evergrn appears to have. In particular, I work hard to minimize base-moves - but I can tell that's not a priority for you, and may even be a counter-priority, so I'll resist piling on on that front .

For a first trip, when you feel likely to return, I'd shade the number of side-trips downward. There is so much to see and do in Tokyo and Kyoto that it's hard to even get a feel for them if you rush through. They are also both so tourist friendly that (IMO) you can kind of live in a tourist bubble the whole time without realizing it if you go too quickly.

I'd be inclined to include Miyajima and Kamakura as my day/side-trips and leave the rest out for this visit. Peace park/museum is a real mixed bag as far as a destination to visit. It's the location of a critical piece of human history but it's also a bit of a downer. Kamakura is a nice, easy daytrip from Tokyo.