Itinerary

We are travelling to Japan for the second time, I am travelling with my husband and 15 year old son.
Can you please advise re our itinerary as I'm conscious that a teenager may not appreciate all the cultural, beautiful scenery aspects as much as me Therefore I want to include some things for him too.
I would be grateful if you could comment on the itinerary and also include some activities for him too (I'm assuming this will be in Tokyo??).
Tokyo 3 nights
Kanazawa 3 nights
takayama 2 nights
Tsumago 2 nights
Nagoya 2 Nights ( May do theme park there)
Hakone 2 nights
Tokyo 4 nights

I'm 20, not too distant in age. I just got back from Tokyo a couple weeks ago and really enjoyed these places.
Akihabara- a huge electronics district in Tokyo, tons of arcades, anime goods, also a good place to buy video games. There's a really cool shop called "Super Potato" you should check out if he's into video games.
-Odaiba - Awesome man made island in Tokyo. There's a Giant Gundam (18 meters tall) that lights up at night with music and a projection screen. Also there is a Toyota museum (free) with lots of cool cars and a driving simulator. I didn't ride it, but there is huge Ferris Wheel there as well.
-Harajuku - Cool place to walk around for teens. There's a really great Okonomiyaki and Monjayaki restaurant called "Sakuratei" there too.
-Tsukiji Fish Market - Huge fish market completely packed with people and street vendors everywhere. It's a great place to get some (very) fresh sushi.
Hope this helps a little !

3 nights in Kanazawa is a lot, especially given that you're also spending 2 nights in Takayama. I'd take one day from Kanazawa and add it to either Tokyo or Osaka and use it to visit a theme park (either one of the Disney ones in Tokyo, or Universal Studios in Osaka).

Rather than two nights in Tsumago, how about one night there and one in Magome (1.5 hours walk away on the old Nakasendo route). Or some time in Matsumoto?