I was on the Superman boards and ended up talking about Trek. So I figured I'd come here and share my thoughts.
This film won't be rushed. Paramount and the Producers have to know they have a hot hand after Abrams Trek, but a lesser sequel could ruin all that because it's still Trek and it's not bulletproof with non-trekkies. It could bring the stigma back. These men seem smart enough to know they cannot mess up and are searching for perfection. They also don't know if Abrams will direct this time, which would possibly dictate the script that is chosen.
If Abrams only co-writes and produces while turning over the directing duties, I keep hearing that Matt Reeves will take up that task. But I think a better choice would be Jack Bender. Bender directed more episodes of Lost than anyone else and as such he has a great relationship with Damon Lindelof from Lost and is now helping to write this script. I know my notion of having a television director take on a studio franchise with a huge budget will leave me open to mockery but I stand by my opinion. The episodes of Lost that Bender directed were the slickest one's, had the best character stories/moments, and great action for a television show. Give the guy a chance, he could pull a Nicholas Meyer without trying to follow up a dud like Star Trek: The Motion Picture.
As for storylines, DO NOT use Khan. That would more than likely be underwhelming and as we said, that can't happen. Either go the safe route and introduce Klingons. That, or does anyone remember the episode of Voyager that saw Voyager come across evolved, humanoid Dinasours. To hell with this episode already using this storyline. No one gives a **** about Voyager anyway. So I propose that the movie features the Gorn from the original series episode "Arena". And have the Gorn be revealed as humanoid Dinasours. I know is also a knockoff of the original series, but with the advancement in film technology and the added dinasour storyline would blow the original episode away.
As for the final film in a possible trilogy, use have Kirk and the Enterprise go up against Section 31. Somehow, find out that Section 31 caused Romulus to explode in the 24th Century and altering the timeline. The Enterpise crew then sets out to stop Section 31 in the 23rd Century and restore the original timeline while savivng Kirks father along with Vulcan and Romulus.
I don't like the idea of using humanoid dinosaurs or Section 31. Section 31 was a Deep Space Nine phenomenon. I'm not fond of classic Trek taking villains/aliens from the later series. It almost suggests they have nothing good of their own or can't come up with a new villain/race. Section 31, without the likes of Bashir, Sloane etc in the mix would seem like something completely different... so why not use something completely different?
Abrams, I think, doesn't want to use the Klingons as villains, because he doesn't want to "demonize" them again after they've been shown as heroes (or allies) later on. It would be a step backwards. Of course, that doesn't mean that there can't be a rogue faction of the Klingons, or a group who don't see eye to eye with the Federation.
The Gorn aren't bad as an enemy, but I don't think I would want to see a CGI villain to be honest. It would have to be a man in a suit or with excellent make up to take me completely out of the story. In "Enterprise", I think they tried to do a Gorn at least once using CGI, and it didn't look very good at all. It ran about without any weight and did look more like a dinosaur from Jurassic Park or something.
There are other enemies Kirk and Co can fight, without it having to be someone like Khan. Some have mentioned that there aren't many left and cite the likes of Trelane or Harry Mudd. Well Trelane could be updated into a more sinister, Q-like entity, and Mudd wouldn't have to be a full villain but just a rogue. Nevertheless, there are other characters who could be villains like Galt ("The Gamesters of Triskelion"), Gary Mitchell ("Where No Man Has Gone Before"), Captain Ron Tracey ("The Omega Glory"), or Balok ("The Corbomite Maneuver") to name but a few.
I know Balok turned out to be just a scary stand in for that baby-looking alien, but that could be changed here. I always thought it would be cool if the scary Balok could have been an actual villain. His ship was also invincible, like the Borg, and was only able to be brought to a standstill by Kirk's "corbomite maneuver"). Having Balok would give us relentless, almost unbeatable enemy without having to resort to the Borg, and keeping it within classic Trek lore.
Or there's always the Tholians.