There's still so much untapped from the comics. Proteus is actually one of my favorite stories so that excites me a lot. Proteus alone probably wouldn't carry a movie though, especially coming after Apocalypse. I think Proteus mixed up with the Friends of Humanity and a reactivated Sentinel program would be a great film.
Then, over in X-Force have them deal with a returning Apocalypse and the Legacy Virus.
Back in X-Men, start focusing on the galactic material. The Shi'ar Empire, the Brood, a cosmic-related Phoenix (maybe a two-part film that brings in X-Force to help in part II).
Beyond that? There's Genosha ("X-Tinction Agenda" was actually my favorite story of the Claremont run), the Phalanx, the Reavers (with a proper Lady Deathstrike, perhaps in an adaptation of "Fall of the Mutants"?), Magneto and the Acolytes.... there's TONS yet to touch on.
And you know how you introduce Mojo's World (and thereby Longshot)? Have a Deadpool movie cover that, so the tones fit together and that way Mojo's wackiness doesn't have to dilute the serious main franchise.