It's likely that the Klingons will be in the next film, though I am not one clamoring to see them again after Into Darkness. I like Klingons just fine and am enjoying them in the "After Darkness" comic but when I think about Trek movies in general the Klingons have been the major foes or prominent adversaries in nearly half of them (Trek III, IV, V, VI, VII, and they had notable cameos in I, IV, and XII).
I wish they would move on to other species like the Gorn and the Tholians as bad guys. I also wouldn't mind seeing this reality's take on the Romulans. The Borg. There I said it. I've always wanted to know how Kirk and crew would fare against them, and if Archer could face down the Borg I don't see why Kirk couldn't.
I'm curious to see what Abrams, etc. could do with a new alien adversary though there are so many existing ones already out there that could be developed and probably serve whatever purpose a newly invented one would.
As for the crew:
-Building on the Carol Marcus-Kirk relationship.
-Developing Uhura as more than Spock's girlfriend while also continuing the relationship.
-Moving McCoy beyond being snarky.
-More development for Sulu, Chekhov, Scotty, and Keenser. Badass and comedic moments are fine, but I liked Scotty standing up to Kirk, it was really the heart of Into Darkness for me, and I would like to see all of the people who aren't Kirk and Spock contributing to the moral and intellectual quandaries the ship will get into.
-M'Vess and Arex added to the crew.
-More names and species names for alien crew members of the Enterprise. I think they are messing up an opportunity for toys, games, comics, etc, by not developing some of those background characters.