2. Explore Different Timelines/Realities
If things go on as expected in this movie it's quite possible the game changer of the entire franchise. Not only will it explore a concept as complex as time travel (one that could bring huge trouble to a franchise like this one, not to mention that it hasn't been explored on a superhero film so far) but because it will introduce the idea of parallel universes and different realities. As usual whenever a film explores themes like that it could go one of two ways; it could go incredibly well and expand what can be done for the story, or it could be a complete piece of nonsense that could destroy the franchise. While this could be a risky move for them, Doctor Who proved to all of us that time travel and exploring alternative realities can give rise to a world of potential. Done properly, the alternate reality slant could do something similar for future X-Men sequels. You could have 2 different franchises going on at the same time, as was initially hinted at when Brian Singer was lined up to release a follow-up to The Last Stand: one with the new timeline with a young Xavier and Magneto when they prevented the mutant apocalypse and another one in the apocalyptic future that will be shown in the film, with the few remaining X-men trying to rebuild their lives and world.