Everything from all the MCU movies vs everything from all the X-Men movies(including The Wolverine).
This is under the assumption that both sides have been taken to a world that is basicly like the real life Earth except with no population and made to fight until only one side is left.
To make things interesting, no mind manipulation powers of any sort will work for the duration of this war.
Both sides get all the heroes and villains, as well as fictional organizations presented in their continuity(for instance, Marvel includes SHIELD, Hydra and the Chitauri invasion force, while X-Men includes Striker's forces, and both the 70s era and future era Sentinels).
So, who wins?