Help to plan family trip

Me, my wife and our two kids (1y&4y) have started to plan our first visit to Japan. We will go in the beginning of Sep and it will be a 14 days trip including Tokyo, Hakone, Kanazawa and Kyoto. I would gratefully appreciate any suggestions concerning.
- Places which kids would love.
- Suitable accomodation and restaurants for kids only used to european food :-)
- Suitable ways to travel with kids in japan.

Thanks
Henrik

Hi, I think you should give Kanazawa a miss and concentrate on Tokyo and Kyoto. (Kanazawa is a bit out of your way) While basing yourself in Tokyo, you can take a day trip or overnight trip to Hakone. While in Kyoto, you can visit Osaka and Nara. As for transportation, I recommend landing in Tokyo (Narita Airport) and departing from Kansai International Airport (near Kyoto) or the other way around. Between Tokyo and Kyoto, shinkansen (bullet trains) is the fastest and most comfortable method.