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1. Alright, we get it already, Khan isn't white.
So I think a major problem with STID isn't just that Benedict Cumberbatch is playing Khan, but that Khan himself is just a generic megalomaniac type. Spock actually has a line reminding him that his goal is ethnic cleansing. All and all, I have to think the villain would be better if he actually were a newcomer to the franchise. So let's start off.
Okay, after the destruction of the USS Kelvin by the Narada, Starfleet was in an uproar. ONE SHIP just owned one of theirs for free, and they must know it could do the same to the entire fleet. And that's if there's just one of them. And, oh yeah, no one knows where it is. We the audience know that Nero is in hiding/captured by the Klingons during this time, but Starfleet doesn't. For all they know, tomorrow the Narada's going to warp to Earth and nuke Australia. This is not a good time to be worried about the price of tea in China.
So Admiral Marcus comes up with an idea. Revive the eugenics program that's been outlawed since Khan. And so, John Harrison is born. Trained from birth to be an ideal scientist, soldier, and whatever else Starfleet may need, he's had everything provided to him except a family.
Bonus points: Harrison has the genetic code of a Starfleet officer, just enhanced. So he could be a clone of Khan himself, or one of George Kirk (making him, in effect, the man's son and Kirk's brother), or Christopher Pike, or Admiral Marcus. It'd be easy to go too schlocky on this, so I'd restrain it to him being Marcus's clone and raise a few issues about cloning. According to most regulations, raising Harrison as, well, Ender Wiggin would be illegal, but there's a loophole--as a clone, he's technically an extension of Marcus, and the elder Marcus can do as he likes with him. You know, sci-fi stuff.
This is why the NuTrek technology differs so much from TOS technology, by the way. Harrison invented it, working off scans of the Narada.
But anyone who's read Frankenstein knows what comes next. Harrison gets lonely and demands that more like him be made. Marcus is worried enough by one of him and smacks him down. Harrison escapes and goes after the Botany Bay, filled with Augments like himself--his 'ancestors'. And it's in Klingon space. Earlier I suggested that instead of being a terrorist, Harrison could simply be selling valuable state secrets to the Klingons. Well, this is what he wants in exchange.
From there, you can build-up to Khan showing up in the third movie without the second movie's villain being 'Khan Lite' (a danger if John Harrison is simply a follower of Khan). You could even have Khan woken up in the third act and ally with Kirk to stop Harrison.
Oh, and as a mad scientist, Harrison would've actually been the guy who designed the Enterprise. That would be interesting. Imagine him breaking out of his cell and running around sabotaging the ship while they're on the run from the Klingons.
2. No future selves in da club
Back in 2009, the original reboot Star Trek had a cameo planned for William Shatner, but couldn't figure out a way to organically fit him into the story. So they shitcanned that. Fast forward four years, and STID decides to drop Old Spock into the story simply to sell the audience on how bad a dude Khan is. This after giving Leonard Nimoy a respectable send-off in Rebootrek, literally safeguarding the franchise's history while Quinto and crew went off to have new adventures.
So, short of deleting that scene so there's more time for Benedict Cumberbatch showing, why not give it a point? Perhaps Khan is dealing fairly and honorably with Kirk, until they get the "warning" from Nimoy that he can't be trusted, so Kirk phasers him in the back and Spock blows up his ship, leading to a vengeful Khan—exactly the predestination they were trying to avoid. After the first film was so bent on destiny, why not spend some time on how that can be a bad thing, and lead someone who could've been saved to instead be an evil space maniac?
3. Maybe the first thirty minutes of the movie should have a point.
So in the first thirty minutes of STID, the crew has an exciting adventure breaking the Prime Directive, Kirk is busted back down to cadet, then assigned to the Enterprise as first officer under Pike while Spock is transferred to another ship.
None of this has anything to do with the rest of the movie. Sure, Pike's death technically puts Kirk back in the captain's seat, but Kirk would've been just as vindictive if his friend had died in any other way. I know it's Star Trek and you need Kirk in command gold, just like a Spider-Man movie can't have Spider-Man losing his powers and a Star Trek movie can't have the crew commandeer a Klingon bird of prey and travel back in time to the 1980s to save a whale… or, you know, those would be the most popular installments of their franchises… but don't tease a tweak to the status quo and then jump right back to another day at the office.
How about this—Kirk is court-martialed for his actions, but it's a ruse by Marcus to give them plausible deniability. Now that Kirk is an "ex-Starfleet officer," he can go after Khan to his heart's content, maybe with a few other members of the crew—say, Bones and Uhura, just for maximum pathos. Meanwhile, Spock and Pike are on the Enterprise, trying to bring Khan in peacefully. We can explore both sides of this moral dilemma, with Kirk wanting to bring Khan to justice, but Spock having another objective—perhaps striking a deal with Khan, amnesty in exchange for, you know, some McGuffin. Or preventing future attacks. The audience can ask what's more important—getting justice for past victims or preventing new ones.
4. How about Klingons, genius?
I actually really liked the scene on Kronos up till Khan showed up. Uhura was getting something to do, getting the Klingons on their side by playing the honor card and literally talking to them in their own language. I know it's hard to give the communications expert something to do in a whiz-bang action franchise (who mourns for Cypher, X-Men comics?), but that seemed fitting. Maybe the Kirklings could've teamed up with a badass Klingon to hunt Khan down—a reboot Kor, for instance, though there's no requirement that he be a TOS character—and that could've laid the seeds for this ally being an enemy in Star Trek Into Klingons Fucking Your Shit Up. The audience could've see why the Klingons are such a big deal. The whole plot is based around the fact that Klingons are scary motherfuckers, after all.
But no, Khan shows up and goes boom boom pew pew bang, then he surrenders to get put in a glass cell because he's a supervillain and that's what they do in the new millennium.
5. Oooooooor this could've been a movie about Khan.
One huge problem with STID is that the need to keep Khan's identity a secret jumbles up the whole plot. We basically start the movie with him having done all this interesting, cool stuff, but not getting to see it because that would give up the game. So we just get to hear about it. And as good an actor as Benedict Cumberbatch is, he's not that good.
The reasoning for this is that knowing he's Khan would have the audience be one step ahead of the characters, going "Don't open that cryo-pod!" Which is, you know, the very reason you would pick a name value villain like Khan, so people know how bad he is. The same way Batman Begins ended with the Joker's card, so people started going "Holy shit!" If J.J. Abrams had directed The Dark Knight, the villain would've been a bank robber named Alistair Simms, then when he was caught halfway through the movie trying to kill Harvey Dent, he'd smear some white paint on his face and say "Some people call me… THE JOKER!" Whatever you say, Alistair.
So, if the movie's about Khan being woken up from deep sleep to fight the Klingons, why not have our main characters be involved instead of hearing about it after the fact? The opening sequence could've been a dangerous setpiece of our heroes getting to the Botany Bay through a plasma storm or whatever and freeing Khan because they need him for a mission. Say, the Klingons have taken a Federation science station hostage (with Carol Marcus onboard, natch) and they need a badass with no connection to Starfleet to free it. The Enterprise crew could've been the ones debating the morality of using Khan; and they'd feel responsible for what he does after he inevitably goes rogue. Let's say Khan exploits some Klingon ritual, challenging the Klingon captain to a duel, then beating him handily and taking over. Suddenly, the Enterprise has to deal with their own rogue operative, who has his own army of Klingons and a hard motherfucker ship.
This is where the Leonard Nimoy cameo would actually prove useful. Spock is suspicious of Khan, calls up his old counterpart and guilts him into giving spoilers. He's told they can't trust Khan; but that was the old, vengeful Khan. This is a younger, less-crazy Khan who just wants to do this job so he and his men can live in peace. But this bit of temporal paradox leads to Kirk trying to stab Khan in the back, so Khan goes apeshit and all hell breaks loose.