The prospect of an arc of some kind running through ST12 and ST13 is the best news I've heard today. Hopefully, there will also be some sort of antagonist character that would also appear in both of them, bridging the two installments, like Mr. White in the last 2 James Bond movies.
To add to the Year One feel, you could have Carol Marcus as a love interest for Kirk, and establish the rivalry with Scotty and Lawrence Stiles (see ST3 and the Prime Directive novel, which is a favorite of Rob Orci, very good read). The scene in PD where Scotty gets mad at Stiles and breaks his prized "swagger stick," one could definitely see Simon Pegg's Scotty doing something like that. Remakes of Space Seed, Arena, Balance of Terror, et. al. should probably be avoided.
Klingons: You can have Gorkon voicing the hope of peace between the Empire and the UFP, with Duras representing the rapacious, expansionistic side. I think Nero stirred up a hornet's nest with his actions in Klingon space, with the Romulan Senate being pretty hard pressed to provide some kind of evidence that Nero had nothing to do with them. Then there's the matter of the resources that the Klingons lost fighting Nero, they may make excursions into other territories in an attempt to replenish them.
As for the Romulans, the Tal Shiar is something that few have played with, and Section 31 is a worthy opponent for them. John Le Carre wrote a trilogy of novels devoted to the long running conflict between his literary creation, George Smiley, and his KGB nemesis, Karla. The first and third novels were adapted by BBC, with Patrick Stewart as Karla. So if a Trek movie had a similar type of conflict between a Section 31 director and a Tal Shiar spymaster, with the Enterprise caught in the middle, that could be the "cerebral Trek adventure" and "real Romulan movie"(as opposed to Nero and Shinzon) that many are waiting for, and that could have enough momentum to carry into a subsequent film.
And of course, there's the Tholians. They're powerful, mysterious, "alien," and one could see them in adversarial situations where they, not are heroes, are the ones that are "right." Plus, no need for celebrity guest stars. Just CG work (going with the spidery appearance in ENT) with Frank Welker doing the voices.