Kingdom Hearts is about original characters exploring Disney worlds. That's not what you're proposing that Nintendo does. The Square-Enix characters are peppered in as fanservice, but center state is all about the original protagonists and Disney characters.
What Squaresoft did was find a way to get themselves in the door with Disney with a co-created franchise, instantly propeling themselves to new, unmatched heights as a Japanese video game developer/publisher. Sure, the partnership helped to keep Disney much more hip and relevant, primarily in Japan, but this was a much bigger and more important deal for Squaresoft than it was for Disney.
Studio Ghibli doesn't desire to entangle their IPs into video games, and Nintendo doesn't need their IPs. This isn't a match that would truly benefit either company in major way, and is a completely different scenario than what happened between Squaresoft and Disney.
Also, as a gamer, do I want to explore and solve the mystery of Totoro and their forest, dogfight with Porco Rosso, tip toe through bookshelf's and doll houses of Arrietty, explore the seas of Ponyo, and make a living in the bath house of Spirited Away? Hell yes. Do I want to do all those things as Nintendo characters? No, I want to play as characters who would make sense being in those worlds and not detract from their graceful beauty.
Original characters such as Sora, and classic Disney characters such as The Fab Five make sense traveling to other Disney worlds, and those worlds are already loud and zany, so they can fit right in with some wardrobe retheming. If we were to have one chance to explore the worlds of Ghibli in video game form, I want them pure and deep. Give me an original human character that jives with the Ghibli art style to travel between them, sure, but not Mario and the gang...
