This whole "the X-Men are moving to San Francisco" thing seems like such an arbitrary, random decision. The reasoning seems to be that, since mutants are a hated race that is continually prejudiced against, the natural place for them to move is the open, accepting San Francisco. Fine, I guess, except moving to SF has done nothing to change their situation? Right away after moving they are set upon by a gang of mutant-hating skinheads lead by the Hellfire Club, who I guess is out west, too. So, moving to this progressive city didn't seem to do anything to drive away the threat of hate and violence, since that only lasted about 2 days. There are no actual changes to the the way the X-Men operate except that they're in a different time zone.
Beyond this, the storyline with Magneto showing up is some of the dumbest, most wasteful storytelling I've seen in a long time in X-Men. We've been seeing Magneto in fleeting glimpses since House of M, still powerless, trying to regain the foothold he once had in the mutant community. So in this one he just shows up and starts fighting the X-Men for no apparent reason, and is soundly defeated pretty quickly. The implication is that he has other plans, but we're given absolutely no idea what they are, so it just kind of slips past as a massive anti-climax.
The rest of the book, while not really fitting the whole San Francisco thing, is decent. The X-Men have to fight a powerful empath who is committing hate crimes against his own people. The story's really straightforward, but it's got some classic X-Men team action that's plenty fun to see, so I'll give it a pass.
The remaining short stories culled from the central Manifest Destiny series range from lackluster to terrible, but luckily they only make up the very tail end of the book, and feel more like a bonus than anything else. So, skipping those is a definite option.
Overall, I just feel like Brubaker had no idea what to do with the X-Men. This book is the final one of his run, which never really did anything interesting outside of the massive crossover Messiah Complex. He's not a soap-opera guy, he's an espionage, black ops, and crime guy. He felt very out of his element for this run, which is very disappointing. I'm interested to see what Matt Fraction does with it from here on out.