It was part of the deal/contract Disney signed when buying Marvel since Universal already had those characters at Islands of Adventure. So Disney can't use them east of the Mississippi River (but they can sell Marvel merchandise).
I am still trying to reconcile Marvel into my idea of Disney parks. I had the same trouble with Star Wars and Indy at first too. I still don't think they quite fit, but that's okay because I enjoy them. Since the very beginning, Uncle Walt had all kinds of things in the Disney parks that he thought guests would find fun and entertaining...and a lot of them were not exclusively "Disney" either.
I think Marvel is a bad fit in MK and IF Disney had the rights to using Marvel in the Florida parks (and they don't, so this is all hypothetical) then the only place it would fit in my eyes would be DHS.
In California, I think Marvel stuff can go in DCA or be used in a third gate. I really don't want Marvel coming to Disneyland but I have a feeling that a 'Stark Expo' might actually happen in Tomorrowland. That kind of fits, though. Tony Stark is the son of someone who was based on Howard Hughes and I think there's a little of Walt Disney in the original Mr. Stark character too (in one of the movies, they showed the design for a City of the Future that was clearly based on Epcot).
If it was handled correctly, maybe Tomorrowland could be all about a character like Stark showing us what the future could be...and this "Stark Expo" could be the queue for the E-ticket ride that would be like a test flight on some new Stark=designed vehicle that would fly around and in it you'd encounter all the Marvel characters somehow.
That would definitely fit in with "Tomorrowland" even if I would prefer the Marvel characters got their own park as a third gate.
