The big plot twist in House of M is that it was Xavier who manipulated the Scarlet Witch into creating the new mutant friendly reality, not Magneto.  This could tie in with Joss Whedon's big "reveal" that Xavier is not always such a nice guy.

Update: I'd like to apologize to my imaginary audience for some of the trolls in the comments.  If friendster's blog technology were halfway decent, i could do something about it.

Fucking Joss Whedon.