Alright, I had this theory worked out in my head, but now I think I've forgot it. So I'm going to attempt to think about it.
I think that Tony Stark/Iron Man is the traitor. Through and through. Fury kept mentioning while pounding at Cap that, "You guys thought we were stupid." Meaning that there's more than one. And then soon after that there's a scene where Tony is getting hassled for building a war plane far beyond military technology. Suspicious no? Millar has mentioned that there will be an Ultimate Red Skull and an Ultimate Ultron. I think Pym is working for the traitor, in some way or another, either that or the traitor is going to steal Ultron from Pym. Now, for Red Skull. Skull might be in league with the traitor, or is one of the friend's Loki mentions is working with the traitor (which basically means the same thing). Skull, at least in 616, is known for taking up identities. And in 616, the Skull that was just recently killed was a clone of Cap. So, back to Ultimate universe, Skull could be impersonating Cap to set him up as the traitor. I'm a little confused about the whole, the Cap we know isn't the real Cap, which, in theory, could mean that the fake Cap is the Red Skull in disguise. I seem to be repeating myself. Now figuring out who or where the real Cap is, I really want to know, I really wish this book was weekly, or at least, wasn't late.
So basically. Stark and Skull are working together and the Skull is a friend of Loki's...or something. Skull is impersonating Cap, and Cap is being set up. Though, I never really read an issue through thoroughly, Fury did mention that Stark's deep sea people found Cap. Which, well, my theory isn't wholly worked out and I need to fix it up more. But there's the gist.