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.
I also have a bad feeling that there will be a Pon Farr subplot for Spock.
I don't see pon farr in a film. pon farr seems to be more suitable for a TV episode.
JJ's films are very fast paced, there is just so much going on.
In a 2 hours film like STiD, ST09 or ST 2016. I doubt there can be a subplot for Spock going into rage mode because he needs sex.