They are at the point now where they need to literally leave the planet. Maybe the next crossover event should X-Men Exodus where they leave the Earth completely. Let the humans deal with Apocalypse and Mr Sinister and the Shadow King. Let the villains have free reign against the humans while the mutants leave. With their combined powers it would be possible to set up a colony on Mars even. They would be able to construct a bio dome faster than any humans ever could and they would be free of the human race. I would love it if they did something like that and everything falls apart on Earth because they leave all of the overpowered X-villains on Earth to do whatever they want to the human race.
They did that with the inhumans when Earth's atmosphere was killing them and they had to go to the Moon. They were just attacked by aliens, the Kree and Morgan LeFay until they had to return to Earth to be attacked by the world's governments then Thanos. The Eternals were attacked as well. Mutants are a species. They could have a refuge, but they should just be able to live amongst humans/inhumans. I think Marvel thinks the easiest way to write stories for species is having them in constant peril because having them live in peace would be like Earth having no villains.