When you are in Kyoto, go to the temple right down the street from Kyoto Tower. The pigeons will fly around you and land right in your hands. Or on your shoulder.
And some temples there have little baby deer that walk around and you can feed them from your hand.
And if you climb Kyoto Tower you can see an amazing view of the old capital city.
Also, there is a comic book shop called Big Boss right up the street from Kyoto Tower. They have all kinds of crazy Japanese comics and art.
At Mount Fuji, there is a trail that you can climb right up the mountain. And then you can buy hardboiled eggs there and eat them as is custom.
Also, Tokyo Disneyland is pretty cool. It is the only Disneyland I've ever been to.
But if you get a chance, go to Osaka. You can see the Yakuza and the Speed Tribe motorcycle gangs ride around the streets and there is a lot of fun stuff to do all on foot.
Also - if you like Hello Kitty - there is an actual Sanrio Hello Kitty Land, that is bizarre.