You could work X-Men back in easily. In the Marvel Cinematic universe, The Avengers are the first superheroes. As with most superhero films really, but it feels more monumental here as if a 'super group' has never been done before. Have mutants be a great big governmental cover-up, plenty of setup with SHIELD squatting on many a secret, and basically this spark off friction from within mutants to 'out' themselves. Professor X would want to show his adopted youngsters can be heroes just as much as Iron Man or Captain America, while Magneto would be seething with bitterness and resentment that powers are now seen to be glorified by the public at large rather than something to be hidden away and their possessors as freaks.
Fans would have to accept however some massive liberties being taken with the modern day time jump simply not allowing for Erik to be a world war 2 survivor, and take their pick from more modern day ethnic cleansing disasters for his origins. As great a job as McKellen did, an elderly Magneto just doesn't have that imposing punch that a buff and furious looking 30-50 age bracketed villain can flare onto the screen, and any youth serum routes are already a bit eye-rolling as a basis.
Better yet, if they did get the X-Men license back (they wont, so I dont even know why I'm torturing myself here) they could setup the whole MUTANTS ARE SECRET thing with Scarlet Witch and Quicksilver in an Avengers movie. Have something go horribly wrong with them or rather all the other non-mutant heroes get press coverage for saving the world again while they did lots of the real dangerous shit but have to stay in the shadows, and now Magneto's pissed and ready to out mutants altogether.
When the funds have accrued high enough Feige, call me.