In an interview with HeyUGuys, and if you didn't watch Star Trek into Darkness there may be spoilers for you. Star Trek scribe Damon Lindelof not only revealed who may be the bad guys for Star Trek XIII, but also talked about the Borg and Q, and a potential crossover with the prime timeline.
In one part he says:
?You can never see enough Klingons, and I think in this film we?ve given the audience a little taste, but there?s also a promise that there?s a larger conflict on the horizon, and that would be fun to see.?
Then a question about Khan:
?To answer that question would be to determine whether or not he actually survives this movie, but if he survives this movie, I think that we would be incredibly stupid to not use him again.?
?You can?t talk about Trek and not talk about the Borg, and certainly about Q. Very iconic adversaries from The Next Generation which is, outside of the original cast films, was my entry way into Star Trek, so I wouldn?t mind getting ? towards the end of our run on Star Trek, maybe baby Picard could be born. There has to be some sort of crossover we?re not thinking of.?
1. Let the Borg rest in peace, please. They've been abused enough.
2. I don't see Q working in a movie. He's fine in an episodic setting, where his meddling is usually intended to prove a point or something, but having an Omnipotent Being sitting around being smarmy would suck all the drama out of a major movie.
I think my main problem is, I don't see Q as an antagonist. Yes, he is arrogant, meddlesome, and annoying. But I always found a certain benevolence to his mischief.
In nearly every encounter with Q in between all his crazy nonsense, he does seem to help.
Making Q some mustache twirling megalomaniac, might be fun in the short term. but I think it would ultimately not feel like Q (unless he is doing the whole mustache twirly thing just to get a rise out of Picard. I can totally see him doing that.)
I still groan everytime I remember the JJprise rising out of the ocean and zooming across the sky at a couple of thousand feet above the ground.
I'm not sure I follow this. Is your concern about the ship operating in other environments than space? Tomorrow Is Yesterday established that the original Enterprise could still function in an atmosphere.
I'd personally wish them to leave the alternate universe separate from the prime now, unless they are either going to move Spock Prime back to the prime universe, or they are going to end by wiping out the alternate and completely re-establishing the prime as the sole timeline. Neither sounds likely.
Borg are a trickier matter. TNG suggested the first encounter was due to Q's meddling with the Enterprise. Voyager retconned that to say the Borg had apparently been picking up ships and small populations of Beta and Alpha species for years before. I'm not sure I'd like the Borg in Kirk's era though. It might require another deus ex machina of information from Spock Prime. Best to leave the Borg for altered TNG.
Klingons are the classic enemy and have yet to truly be shown in full force in space. I say bring the 5 captains into the picture: Kang, Koloth, Kor, Gorkon, and Chang.