My guess is that the Klingons will be the primary antagonist in the third film. I also wouldn't be surprised if they brought Kahn back into the mix. Perhaps with the Klingons stealing the cryotubes of Kahn and his people with the intent to exact revenge for the death of their squad of warriors or maybe to even take a second crack at creating Klingon augments (ala the augments from Enterprise or something). Either way, it will make for another big action-Trek film.
Personally, I'd like to see Kahn left out of it for a third film but I really doubt they'll do that considering how well received his character was in STID. My dream film would be to have a war with the Klingons and to throw the Romulans into the mix somehow. Maybe with them kidnapping Spock Prime with the intent on learning more about the future for their own benefit.
EDIT: BTW, not that I'm hoping for it, but I wonder if VGER will play any sort of a role in another film. It's assumable that VGER is on it's way to Earth despite the alternate timeline. I wonder how the crew would react to VGER in the NuTrek. If you want a little Borg action, and if you like what Shatner did with VGER in his books, you could have VGER try and assimilate Earth or something.