Nara is awesome. Though you will come to realize deer are fucking STUPID. Get the yakitori if you go, they kick ass at it.
I'd say target Kyoto over Tokyo because tbh like 95% of the tourist areas in Tokyo are just shitty sexpat sex districts when they aren't soulless shopping centers like Shibuya.
Maybe Akihabara is worth it for both the really cool electronics markets they have that make Kowloon Walled City look spacious and planned out, and because that's a local heavy metal scene. All sorts of really cool instrument and record shops in that neighborhood.
Hiroshima's nuke memorial is very powerful and worth a visit even if a lot of it is historical revisionism on how bad Imperial Japs actually were.
Onsens are horribly overrated and mostly a lot of ugly old people looking uncomfortable, would not attempt again
You are probably going to see some ancient Japanese couple change JR train cars if you deign to sit near them so be prepared for that.
OH and find a reason to get a haircut, Japanese barbers are something else, legit the best haircut experience I've ever had. TBH the shave was more amazing than the haircut, I've never had a better one, there wasn't a single hair south of my eyebrow by the time that lady was done with me.
EDIT: People also meme about the sushi in Tokyo's various train stations but I'm going to be honest, you could probably fetch something equally amazing, weird, and delicious at a random truck stop that borders the Sea of Japan for 1/5th the cost. Pretty sure the best sushi I had in the entire country was in Toyama.