Cyclops was right. The final issue is nothing but proof that Cyclops was 100% correct in the first issue of "Avengers vs. X-Men" and, yet, somehow, he became the villain. At the beginning of the story, he told Captain America that the Phoenix was coming to Earth to bring back the mutants and use Hope as its host. Captain America called him crazy (and with good reason, I might add) and, so, they fought. But, when the Phoenix arrived and was 'broken' by Tony Stark, it possessed five different X-Men who claimed that they were simply holding onto the power until Hope was ready for it, which, again, is true. During this time, the Phoenix Five did a lot of good things, but four of the members proved corrupt and were stripped of their power. However, Cyclops never wavered until issue 11. Up until that point, he continually kept the others in check, told them to be patient with the Avengers, and, generally, only reacted to the violent attacks of the Avengers. In issue 11, he was again attacked and, surprise, surprise, was finally pushed to the point where he overreacted to their attack, killing someone who was actively trying to assault his mind (self-defense?) and, generally, getting really pissed off at the heroes who wouldn't even try to work with him, who automatically assumed him crazy and corrupt… despite the fact that he was right. In the end, Captain America, after having known Hope for all of two weeks, decided that she was more trustworthy than Cyclops, a mutant superhero he's known for years and fought besides dozens of times, and allowed Hope and the Phoenix to do exactly what Cyclops said they would.
Cyclops is the hero of "Avengers vs. X-Men" and Captain America is the villain.
But, I wouldn't say that that's the story that Marvel tried to tell, would you? Which is what I found frustrating. You can't present a seemingly off-balance/crazy character in the beginning like they did with Cyclops and, then, have him actually be right the entire time. They were some hints about that at the end of the event (more in the latest issue of "Uncanny X-Men" than in "Avengers vs. X-Men" #12), but it's a fairly messed up way to present a story and suffers a little from the semi-recent idea at Marvel that Captain America Cannot Be Wrong. No matter what, that's the one character that is never wrong even when he's clearly wrong.