Cyclops won. Awesome.
No matter what Cap says in the epilogue, Scott got exactly what he wanted at the start of the series; mutants are back.
And he's in prison - so what? He was more than willing to die for his cause, being locked up ain't shit. And, as has been pointed out, is so fucking hypocritical it's laughable. If it had been Jean, Logan and Steve would be kissing her ass and practically throwing her a party.
Hell, even Xavier's death can't be that much of a bother considering the old man's actions of the last few years. In death he'll get his sainthood back, and be entirely forgiven for his misdeeds in Deadly Genesis and with the Illuminati. Oh, and no one mention Onslaught, right?
All in all, while the final issue was a bit meh, the ambiguity of the ending is what I actually like about it the most. Though you've got wonder if the next event will address Cap and Wolvie's hubris, the way this one took aim at Cyclops'. Probably not.