My personal preference is to go cosmic. They are introducing the idea of alien and celestial technology in Apocalypse. Go to space and make it as broad and weird as Guardians (though maybe not as post-modern and self-aware). Bring in the Shi'Ar and basically reinvent the tone of the X-Men films.
Then in the one after that, do the Dark Phoenix Saga right, roughly how it occurs in the comics with Jean being able to destroy planets (though maybe she doesn't actually kill a whole civilization Death Star style). Then it is about the X-Men protecting Jean from the Shi'Ar only they don't kill her, because that would be redundant.
Then in the last one of the new cast's trilogy, they come back to earth and due to the physics of relativity, Interstellar style, they wind up the 21st century. Boom, they have now done the stuff comics fans thought they would never do, and they are back in the 21st century to do more earthbound adventures for the first time in a decade.
I think it would be a fun way to differentiate it from the previous ones. Mr. Sinister? Eh, while he looks different and has different powers, he is ultimately just another big bad like Apocalypse, and not nearly as cool of one at that.