I've already said I'd like to see the Klingons and Federation finally have the full-scale war we saw in "Yesterday's Enterprise" and which, apparently, a ****-ton of Admirals would really like to see happen.
I'd also like to see a larger role for Uhura. Part of what I liked about the reboot was we were capable of moving past the original stereotypes of the 1960s but, honestly, it's become even more the Spock/Kirk show than before and that's something I'd like to avoid.
Karl Urban I'd also like to see get a somewhat meatier part than just being the occasional source of snark to the main duo. He really went downhill to focus on the Kirk and Spock relationship.
As much as I'd like to see a moral dilemma-focused movie, I am not so necessarily focused on this I wouldn't want to continue the whizz bang pew-pew action either. Star Trek had been on life-support for a decade and seeing it garner good public will (even as brainless action) isn't a bad thing IMHO.
That and, again, I like the Big Epic StuffTM happening onscreen.