I really have a strong belief that characters should drive the story not the other way around. I think this issue represents that in two ways. Several of the characters act totally out of context to how they have been portrayed in the past, Emma and Magik are nothing like their characters normally act, their speech feels like someone else and just used to bring the story along and accentuate the plot points.
Then you have the big reveal, now this is very much character driven. I can totally see this character acting in this manner, both for the reasons he gives and also because it would just be like this person to act in this manner and turn a situation to their advantage. I'd like to explain my reasoning in more detail but it's difficult with spoiling the reveal.
Art wise, I love Bachalo's art. A lot of people complain about it, in fact my first encounter with Bachalo was reading the Messiah Complex trade. Going from beautiful art to Bachalo's jagged format was jarring and I hated it. But as time as gone on I've come to love Bachalo's art style. It's an acquired taste but me personally, I love it. I just wish the costumes had better designs. Magneto's change makes sense in that Cyclops is now in red, two character's in red doesn't make sense, But Magik's costume is both good and bad, I like that there's a hint of her growing up in her attire but I hate that all character's seem to have revealing outfits. With Emma it makes sense, that's her identity, with Magik it seems like laziness. The other two characters's don't even look properly designed yet.
I hope this series improves, there's clear potential here. But Bendis needs to go back and read up on his Emma and Magik. Go read New X-Men (Morrison and Yost/Kyle runs) there's a start, get an understanding of both character's 'voice' then come back and think how the recent events will have affected those character's as the ones he's wrote here are cookie-cutter female character's. And definitely keep mystery on the big reveal, whether it's for the reasons described or something more sinister, keep it ambiguous I like the idea of grey around that character.