I knew there had to be a plot twist in House of M.  I had it half right: it wasn't Magneto who was behind it all.  But i had pegged Xavier as the guilty one.  Wayne suggested Quicksilver, who has a history of being a little unhinged (it's all Crystal's fault).
The story ends with the Scarlet Witch wiping out the vast majority of mutants from the Marvel Universe (not killing them, just taking away their powers).  This is a huge reversal of the new direction Grant Morrision set-up.  For years, due to Chris Claremont's Days of Future Past and other stories, it was generally assumed that in the future mutants were going to end up being a hunted and persecuted minority and the world was generally headed towards some sort of authoritarian rule.  And throughout the years, we would see signs in the present day universe that showed that things were getting closer to the various apocalyptic futures.  And after a while it really started to be an old story that got boring and predictable (especially in the hands of the crappy writers of the 90s).  And then Grant Morrision came along and breathed some new life into the backstory by introducing this idea of an explosion in the mutant population, so that within a few decades mutants might end up being more numerous than normal humans.  It changed the concept of mutant concepts in a bigger way than most writers probably realized, because instead of being doomed defenders of a lost cause, the X-Men were suddenly the vanguards of a new species.  It was more positive and definitely very interesting (the original Clarement stories were also interesting; make no mistake.  It's just that the concepts dragged on for 20 years, going nowhere). 
But now Bendis has essentially wiped that out (unless he's entrusted the lesser writers involved in one of the follow-up stories to reverse it).  In itself, this is fine.  It's good to shake things up every few years.  But the fact that this was done by a mega-powered Scarlet Witch reality reversal switcharoo is a bad story device and it leaves things open for any crappy writer to do just about any garbage they want.  It also potentially eliminates a lot of good characters (of major characters, so far we've seen that Iceman has lost his powers).  They said that anyone not in the room with the White Queen at the time the Scarlet Witch knocked her shoes together would be affected (why was the White Queen able to defend against a magical reality changing spell?  She's just a telepath).  That means just about EVERY mutant bad guy should be affected: Apocalypse, Sabertooth, the Blob, etc, and lots and lots of good guys, too.   There's no way they'll stick to that.   Or i read it wrong and it was just random anyway..  So it'll start to get arbitrary real fast.
Bendis is a good writer (though this story was definitely on the weak side) and he's writing about half the books at Marvel so he may have figured all this out and plans to develop in a quality way, but i don't think he's writing any X-books, and the other half of the books at Marvel are written by, um, not so good writers, so we'll have to see how this pans out, but i'm not hopeful.