Worth noting also that Hayao Miyazaki and other Ghibli artists came here to research the buildings and gain inspiration in preparation for "Spiritied Away". So there is a strong anime connection, particularly for those who really love this cartoon.

If there is deep love for My Neighbour Totoro then perhaps you could visit the Nihon Minka En. It is quite different to the Edo-Tokyo Open Air Architectural Museum. I like both, but the Nihon Minka En is pretty special and may tick all your boxes.

Manga often open up kids' eyes to different foods. It could be that they haven't understood yet the difference between dried packet ramen and the stuff the Japanese go nuts for. Perhaps the Ramen museum in Yokohama is worth a stop.
If they are into takoyaki, there's a Takoyaki "theme park" in Decks out in Odaiba. Sunshine city has Namja town with all kinds of weird and wonderful games and amusements to try and all kinds of weird and wonderful foods to try.

As for Disney, only one I'd recommend for anyone who has visited the other parks is disney sea. It urinates all over Disney Paris and from every level.