According to Moira, who has lived and died in multiple timelines, mutants will lose in just about every time in the future because humans will use technology to evolve themselves.
Cyclops was the leader of the entire mutant race after House of M for several years, and he became basically a mix of Magneto and Xavier ideologies.
Also in the comic story Xmen vs Avengers
Cyclops turns mad with power when he gets the Phoenix Force. Even Magneto tells him to chill the fuck out. Story ends with Cyclops in prison
That's actually the last xmen story I ever have seen so I actually have no idea what happened after that