We will finally get to see Ultimate Alpha Flight when they make an appearance in Ultimate X-men. The bad news is, it sounds like they will there as the bad guys.
http://comics.ign.com/articles/845/845178p1.html
The exact quote from the second page of the interview:
IGN Comics: The million dollar question: What's your run going to be about? Any specific villains you're planning to use? Any particular concepts you hope to explore?
Coleite: I'm still working out some details and truthfully I want to keep some surprises. But, you're going to see characters do **** that they've never, never done before. I'm really ****ing excited.
For me, the best kind of conflict is internal. The X-Men shouldn't always see eye to eye on every issue. No one ever does. In the end, those nearest and dearest to us are always our worst villains – our greatest nemesis - because we actually care about them. So - actually - there are no traditional villains in this arc. No Magneto. No Blob. No Toad. No Apocalypse. No Brood. Pretty much just X-men. Oh, yeah - and Ultimate Alpha Flight.