My two cents to a possible story.
I seriously think that if they combine the classic Marvel stories to Ultimate stories...Must be a good movie.
They can introduce Xavier and his school with the first students: Cyclops, Beast, Storm, Jean, Emma and, why not?, Banshee. They are also other students but Xavier want that other students studying while these 6 chars learn to fight and put together a team called X-Men.
Meanwhile Mr. Sinister has vision of Apocalypse that explain if wants live forever they must kill 5 mutants. Sinister kill three mutants (maybe Dazzler, Banshee, Polaris?). The X-Men are in search for the truth. When Sinister kill Havok, Cyclops wants revenge. Sinister wants kill Cyclops for last.
It's good if Gambit works for Sinister as a "Marauder" but he don't know what Sinister doing with the mutants he kidnap. After fight, Gambit knows the truth and help X-Men to find Sinister and fight him.
Before Cyclops kill him, Xavier stops and Sinister is arrested. Like in Ultimate comics in the end we hear that Sinister has vision (again) of Apocalypse and these "monster" ask him to commit suicide.