Well, for one thing, Magneto hasn't been an arc-villain in a regular X-book for more than five years now (since "Planet X"), and before that not since "Eve of Destruction" in 2001. He's the X-Men's traditional opposite, and, based on the little teaser appearances he's been making over the last year, he's working on a means of moving beyond the limitations of M-Day (he seems to now have his powers back, for example).
What exactly do you want the X-Men to do, if not deal with the factions within the mutant community?