They got it right with Star Trek 09, and they were somewhat offski with STID so I'm a bit ambivalent. My main concern is where they're getting inspiration from the Star Trek source material; either from movies of TV series or perhaps both. Start poking around TNG, DS9 and VOY; I'm sure you will find something interesting and easy to adapt to the third film.
To be honest I only have three requests of them; more McCoy. Leonard McCoy is not one of my favourite ST characters but in the JJ universe he's one of my favourites simply because of what Kurl Urban has done with this very limited role. If STID gave Scotty more to do, which I liked, then I hope the third film will give McCoy more to do.
The second request would be to place Kirk and Spock a bit more in the background and focus on the other main characters. Otherwise it's going to be the Kirk/Spock show. Consider if Kirk and Spock were opposite ends of a taut string, McCoy would be pulling the centre of the string to get Kirk and Spock to converge. Or at least that's how it worked in TOS. That kind of dynamic or perhaps a foursome of characters would be interesting.
My third and final request is to end the cringeworthy Uhura/Spock romance. It did not work in ST 09 and it got in the way in STID.