Oh, V'Ger and Whale Probe are easily possible. The timeline wasn't affected in anyway regarding those two. Ditto Guardian of Forever, Mr. Atoz, the Iotians, CharlieX, heck, even the Gary Mitchell thing is still possible. Naked Time. The Corbomite Maneuver. The Doomsday Machine. Obession, only has Kirk seen the cloud before or not? Daystrom's M5 computer. Day of the Dove with the anger fed alien. Tholians. Garth. Lights of Zetar. Methuselah. Even the Genesis Device is still in play, as is the not-God, and Praxis exploding, and yes, even the Nexus.
Of course, we'd have to go with the Salt Monster... wouldn't that be a good revisit? Heh. Oh, and definitely Spock's Brain. Have to do that.
Kidding about those last two, by the way...
To me, what would be *very* interseting, and I personally would dearly love to see is the Talosians revisited, as in The Menagerie/The Cage. General Order 7 HAS NOT BEEN ISSUED YET, as Pike never got there. He's dead now, Jim. So if Kirk and company were to somehow stumble upon them? Without the General Order? A little bit more desperate Talosian population maybe due to the closer-to-extinction issue? And Vina as the Orion Slave Girl. Heck yeah. Let's see that.
Although, it's possible they were discovered by another ship... or Marcus got to them, but that's highly unlikely, let's be honest about it. If he had... he wouldn't be there to take the Vengeance out in the first place, I'd bet.
Oh, you want Star Wars/Khan like? How about going after Balance of Terror? Might as well get the Romulans some play, although we already know what they look like and all that. But the same idea.
No? Trelane then. Yep, that'd be fantastic. Or how about Let That Be Your Last Battlefield? Mirror Mirror? GARY FREAKIN SEVEN, people... that had a lot of good potential right there.
Point is, there are SO many TOS episodes and not-yet-seen-in-this-new-timeline characters and/or plots that would work, and work well, if done right. Not even 'with a twist', just reimagined for the new timeline, and haven't yet BEEN affected by the timeline, and won't be, likely. Whatever their story in TOS, the situation with the Federation and Nero would simply not have made any difference to them, so they're still there, awaiting their discovery by the Enterprise.
Having said that... I sincerely hope they go elsewhere for a story instead of taking yet another piece of TOS and mucking about with it. New content. Original. Well, as original as a couple thousand years of story writing will let 'em be.
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Re: 'controlling' Khan. The difference is that Marcus was being proactive, as he explained, in searching for new ways to defend the Federation. And they got to Botany Bay sooner. Figured out what was going on (like Spock did in the original show) with Khan, et al. Decided to hold the others hostage to make Khan do their bidding. That's it. As far as how he go to her sooner... Yeah. That is quite interesting, but if you have enough sensors actively whacking everything possible... a DY-100 class Sleeper Ship would definitely show up.
The problem with the Botany Bay and her whereabouts is this: Some say only 20 LY away from Earth, some say 300, and anywhere in between. As there were no records of the Botany Bay being launched, nor who was in it, the trajectory was not known. Turns out it was towards Betelgeuse, which is 'south east' of Klingon space... according to the maps in Star Trek Encyclopedia, anyway...
Point is... rather amazing that she was found by Marcus. But excepting that, 'controlling' Khan would have been easy as he cared about his fellow ship mates enough to do it... and bide his time. They were safe, just frozen, after all.
Adm. Marcus was a person of which good riddance was deserved (as written). Having Khan off him with the skull crush in front of Carol? A bit horrid, over the top, but pointing out what Spock Prime said "Ruthless and will kill you to get what he wants." (paraphrased)
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Wow. I did carry on, didn't I?
I'd like to say this about Trek movies vs a series on TV (or cable... or even internet)
The problem with a movie is it has to be a heavy hitter, hitting hard, to keep the entertainment value. Long, interesting, intellectual/topical stories like Let That Be Your Last Battlefield do not do well in the theatre. Star Trek is NOT movie material, by and large. Final Frontier, Insurrecton, and Nemesis. All did badly. Especially Nemesis. And yet, Nemesis was about as TNG as TNG got, and Final Frontier was the same for TOS.
But in the big screen... not so much, no. So you have to go with flashy explody tenseness of dramatic. And with a few exceptions, that's not TOS, nor is it really Trek.
It is going to have to be though, if they want to keep this ship afloat on the big screen.
Maybe I shut up now. Heh.