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.
Vger has been dealt with in the comics and is not an issue moving forwards.
There is a lot of things that could be included in the next film, they could visit the Romulan/Klingon world from Ashes of Eden for instance.
I think the next film will be something relatively straight forward such as a Klingon war or perhaps an early Borg meeting. What will really decide the story for the next film is whether it is set during the 5 year mission they have just begun or afterwards when they have returned to the Federation.
It is possible that we could have the meeting between the Enterprise and the Totality which happened in the first five year mission (offscreen) of the TOS timeline but was heavily revisited in the Shatner books.
We shall have to wait and see.