Considering the next film is going to deal with Apocalypse i wonder what they're going to do after, will they stretch the villain into another paralel times type of story with Age of Apocalypse? Maybe Mutant Massacre or Fall of the Mutants? The problem is that those would need a proper introduction of the Morlocks, but with the introduction og the Fantastic Four in this universe, you can use Reed's son.
It's also possible that we'll see a proper take on the Dark Phoenix storyline, Bryan Singer's original idea had the Hellfire Club in the mix, [BLACKOUT]we didn't see Emma actually die, unlike with Azazel and Angel where actually saw pictures of their dead bodies.[/BLACKOUT]
Either way, it would be interesting to see Magneto form Genosha and live there in peace for a long time.