Japanese national here, I was born there and go back every 1-2 years so what I think are good:
Tokyo
-Asaksa
-Team labs (there are 2, both are good)
-Art Aquarium Museum
-Many of the animal cafes (capybara, hedgehog, cat, owl, etc)
Hakone: only been once, but
-Hakone Kowakien Yunessun was a unique experience, wouldn’t recommend staying there though
Osaka: Kinda boring tbh, dōtonbori is the most interesting area, Jumbo-Tsuribune Tsurikichi in Sennichimae is good, I’d spend a day in Osaka just go to Kyoto and Nara from Osaka by one short train
Kyoto is good, I think there’s too many tourists, but Kiyomizudera, Kinkakuji, fushimi inari jinja, Sanjūsangendō, kimono forest