Not long ago, I spent a pleasant afternoon sifting through the archives here and also at ONTD_startrek, and it's amazing how much wrong information and bad rumors were floating around in the years leading up to both JJ Trek films. But having said that...
I believe that the writers have stated that the seeds for the third movie were laid down in STID. So it's probable that the next movie will involve war with the Klingons.
This fits with my impressions -- I do believe the main plot points of the sequel were at least hinted at in STID. War with the Klingons. Carol Marcus. NuDavid is on the way. Maybe even the return of Khan and/or a plot about the lingering affects of Khan's blood on Kirk. And while I don't really see any "seeds" for Ponn Farr, that's a definite possibility too, IMO.
As for JJ, as much as I'd love for him to direct the sequel, factor in pre-production and post-production on both films and he would effectively be directing two movies at the same time. That's nuts.