I believe Universal has theme park rights for Marvel East of the Mississippi in perpetuity. If/when Anaheim builds its long planned 3rd gate Marvel will likely have a large park presence there.
This is correct. Universal owns the theme park rights east of the Mississippi and in Japan (though they only own the Japanese rights for another decade or so - the Florida rights are in perpetuity).
Here's an article that explains the ownership of DC Comics and Marvel rights, if anyone is interested:
http://www.themeparkinsider.com/flume/201307/3558/
This article mentions what I think is one of the funnier aspects of the Marvel rights - Disney can promote Marvel movies on its WDW monorail loops (like it did for "Iron Man 3"), but only on the MK loops, not the Epcot loop. This is because the MK monorails don't enter a theme park, but the Epcot monorail does, & Disney can't use Marvel characters "inside" the theme park!
When it comes to movie rights, Disney doesn't even own all the Marvel characters. This article lists who owns whom:
http://www.comicvine.com/marvel/4010-31/forums/the-marvel-movie-character-rights-and-where-they-a-666672/
"Sony: Spider-Man and Ghost Rider (and all related villains, characters, etc.)
Fox: X-Men, Daredevil, and the Fantastic Four (and all related villains, characters, etc.)
Marvel Studios/Disney: All the characters that aren't affiliated with Spider-Man, Ghost Rider, X-Men, Daredevil, and the Fantastic Four."
AFAIK, Universal owns all the "theme park" rights to the Marvel characters, but even if they sold the theme park rights to Disney, it doesn't mean that they would automatically put them in the parks, since they don't own the movie rights to them.
It does make me wonder how much Disney could "blur" the theme park / resort distinction. For example, Disney could easily build a Marvel-themed resort (or re-theme an existing resort). For example, I could see Disney re-theming one of the All-Star resorts as Marvel.