Namor, his story, I doubt he'd be directly an Avenger, but Atlantas could definitely be involved. Some Invaders action would be pretty cool, too, and I hear they are going to do more WWII stories in future Cap movies, so fingers crossed. And with the whole mutant thing... I doubt it'll be too much of an issue. I mean, it's a plot device. Heroes got away with saying the super people evolved, I don't think Marvel will get in shit for it, and Mutant is a word used for any number of things. I doubt Marvel could have sold the rights for it if they wanted to. And even then, the world that hates and fears them, again, has been used repeatedly in the past by other companies, even if they don't use those words. Magneto's involvement might be a little harder to cover up, but I wouldn't say impossible, the kids have made names of themselves without him. Just being a pair of super powered misfits would probably be enough.
And if Fox does get uppity about Mutants being used somewhere else, it'll be interesting who's lawyers are better, theirs or Disney's.