"Star Trek Into Darkness" co-writer Damon Lindelof says there is already talk about a third installment in the rebooted series.
In particular, 'Into Darkness' hints at the coming of an inevitable Federation-Klingon war. The Klingons themselves appear in the film boasting similar features to their pre-reboot counterparts (albeit with a new look). Lindelof tells HeyUGuys:
"You can never see enough Klingons, and I think in this film we've given the audience a little taste, but there's also a promise that there's a larger conflict on the horizon, and that would be fun to see."
He also says they've considered 'Next Generation'-era adversaries in the series:
"You can't talk about Trek and not talk about the Borg, and certainly about Q. Very iconic adversaries from The Next Generation which is, outside of the original cast films, was my entry way into Star Trek, so I wouldn't mind getting - towards the end of our run on Star Trek, maybe baby Picard could be born. There has to be some sort of crossover we're not thinking of."
At present, the cast is signed on for three films total so a third film seems inevitable at this point, even if J.J. Abrams opts out of directing it. That possibility is looking less likely according to The New York Times.
The paper indicates Abrams' commitment to "Star Wars: Episode VII" may prevent him from returning to the director's chair: "He [Abrams] said it was unlikely that Paramount would wait another four years for such a film, in which case his 'Star Wars' schedule would likely conflict with it."
Abrams producing partner, Bryan Burk, added that Paramount were not happy with the wait between the first two 'Trek' films.