While I think X-Men are better off where they are for the moment, based on the previous output of FF films (which blew hard), and direction this new one seems to be going (which is looking less and less like any FF I'm familiar with), I feel Marvel Studios would be a better place for them. Plus, due to the nature of that team, they fit in more naturally with other comic characters. They were generally pals with all the other heroes, beloved by the public, and Reed was particularly helpful as the go-to scientific genius of the Marvel U.
The X-Men were always freaks and outcasts, even among other superheroes. Plus, they have their own series of offshoot teams and characters (New Mutants, X-Factor, X-Force, X-Men subteams, Deadpool) that could make for a totally complete, intertwined universe that does what Marvel Studios is doing without needing to bring in Iron Man or whatever. And most importantly, at least for now, the film makers understand the franchise, know what they are doing, and are willing to invest in X-films. Would this be the case with Marvel Studios? Not sure. They've got a lot of irons in their fire, and I'm not convinced they could concurrently do justice to all the characters they are currently dealing with PLUS the X-Men.
