Here's how we make a Marvel world work.
Instead of trying to figure out what to implement from decades upon decades of comic books,have it somewhat follow the original Avengers film.
However, instead of the Tesseract summoning Chitauri, have it summon Heartless. Loki is still the main villain. Can't fit the whole movie? Well, Kingdom Hearts II allowed you to come back to every world later on if I remember correctly, for a "second episode" of story.
I remember Nomura saying something about how in this game, characters that may have previously only inhabited the world or been bystanders will join in the fight. This is a great thing. This means you can still have Sora, Donald and Goofy, but with the Avengers appearing in massive set piece battles (just like in the film) and possibly even randomly within the world, alone or as a group, if you happen to be near them.
Do we need a moral, like Kingdom Hearts I actually did very well with so many Disney worlds? Well, I'm sure there's plenty to be had, especially in interactions Sora could have with Captain America. Sora is fighting with older, more experienced heroes who could easily offer him some wisdom.
What's that, you say? It would be weird to have New York City in Kingdom Hearts? And a guy named Captain America? Let's not forget flying around Big Ben in Kingdom Hearts I and Wendy actually referring to London! And in Kingdom Hearts II, even though Mulan's world is called The Land of Dragons, the Emperor tells her she saved China.
In the Avengers film, towards the end of the battle of New York, the heroes are completely exhausted and the tide starts to turn against them. You could easily portray this as even though they're capable of defeating countless Heartless, they don't have a Keyblade to seal the world and thus the Heartless keep coming, eventually wearing on them.
Live action wouldn't be weird, considering we had Pirates and Tron. There's already a precedent. And while Pirates is debatable (although I liked it), I've never heard anyone complain about Tron's implementation.
There's also a ton of potential for weapons to be gained in this world. Obviously Cap's shield for Goofy, but you could have a Mjolnir staff for Donald and Iron Man could offer to make some "upgrade" to Sora's Keyblade, which would give him a keychain. Characters in Disney worlds have given Sora keychains as presents.
And lastly, if you can't get the actors from the film to do the voices, just use the VAs from the current cartoons. The cartoons themselves may not be the greatest, but the voice actors are pretty damn swell.