I went this last November with my son. And a year or so earlier with my wife.
Some thoughts that I came to on this last trip.
1. I am not a fan of Tokyo being so busy, but this last time did find some cool neighborhoods that were along my pace this last time. Jimbocho has some great used book stores, ukiyo-e stores, I definitely didn’t get enough time there. I quite like the area around inokashira park. It has a great shotengai and doesn’t feel “Tokyo” big. Like a part of maybe Nagoya, Hiroshima, or Sendai. Feels not as insane as say shibuya or Akihabara.
2. I really love Kyoto as it was next door to my last area. I went right after Japan reopened and it was lovely with my wife. This last time kinda bummed me out as the tourists were out of control (in amount of people) in every place. Luckily we went early or late to kiyomizudera or fushimi inari. To have some “alone” time. But I did plan that I was going to be intense this time and planned on a lot of activities in shiga-ken(where my last area was). It’s just as pretty as many places in Kyoto and you can avoid the crowds. Hisyoshi taisha, enryakuji, ishiyama-dera, hikone castle, Chikubu-jima.
But the nice part of Kyoto is the ability to jump to Osaka, Nara or even himeji, easily.
Anyways if you just stick to Kyoto for the trip, no Osaka etc, I would to the early morning trek of kiyomizudera and a late night to fushimi inari and find something to do in the middle of the day and you can just keep it to a day or day and a half. Just me but the crowds soured me on it.
Most of the tourists are Chinese and they really are hitting a lot of the Buddhist sites (Todaiji in Nara was straight crazy).
3. I only went once to Hiroshima with my wife and between the atomic park, miyajima, and iwakuni for a day trip, I would love to go back there. Seems like if you know the area and your wife probably would love those sites. You could probably avoid a lot of the crowds that the tourists are causing.

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