Then Star Trek into Darkness came out and it was… a big, dumb mess. It’s simultaneously all the bad parts of The Final Frontier, Insurrection, and that one episode/movie you reviewed where it kept getting worse each time you saw it.
One of the reasons for that is Khan. I actually don’t mind the fact that they used Khan, but it was a mistake for 3 reasons:
1) It justified everything the skeptics said about the creative team not being able to come up with something new and that they could only ripoff the originals, especially with the inverted Wrath of Khan death scene.
2) The use of Khan felt unearned, because it’s too soon to put a crew that’s discovering itself (and being discovered by the audience) against such an overwhelming and well-known foe. There needed to be at least one movie where the Abrams Trek crew worked together as a cohesive team and showed the audience that they were the best of the best, so that when Khan is outwitting them, it honestly feels like he’s superior to them in every way. STiD suffers a lot because Khan is facing off against a crew of rookies, which automatically makes everything he does less impressive.
3) Khan is two characters – John Harrison and Khan Noonien Singh (who was shoehorned in by Damon Lindelof) – and John Harrison is the more interesting character. Even though Harrison is a fairly generic sociopathic genius type character, he’s interesting because we want to know why he betrayed Starfleet and did all those horrible things. But once he’s revealed as Khan, he becomes a scenery chewing villain with little subtlety except in the scenes where he's the generic genius villain (in fact, at one point in the scene where Khan and Spock are on the bridges of their ships, Khan’s facial expression is literally that of an anime character).
As for the rest of the movie, it’s the ultimate combination of bad writing tropes: “competence and pragmatism = evil,” “evil = stupid,” and “good = dumb.” The result is a film that constantly makes me ask the two questions that shouldn’t be asked often while watching it: “why are the characters doing X?” and “why don’t/didn’t they do something else?” It says a lot that the novelization, much like The Final Frontier’s, manages to turn an incoherent mess into something that at least is a passable story with understandable character motives.
For example, consider Admiral Marcus. He is presented as evil for wanting to build up Starfleet’s military abilities after seven ships and a founding world of the Federation is destroyed, which is a totally reasonable position. His orders to kill Khan using the torpedoes are also completely understandable and justified in retrospect by what happens after Kirk fails to kill Khan once they get on the bridge of the dreadnought USS Vengeance. But his plan to start a war with the Klingons isn’t just immoral, but utterly stupid and nonsensical because of how counterproductive it is.
Marcus wants Starfleet to be militarized and I guess a war would force Starfleet to do it, but it would make more sense to pit the Klingons and Romulans and buy time to complete more dreadnoughts and long range torpedoes, while upgrading the fleet with tech developed with Khan’s help. Reinforcing the idea that he’s an idiot is the fact that he and Section 31 had no contingency plans for dealing with Khan, didn’t foresee Khan betraying them and insert a bomb into his body (Escape from New York style), didn't think of killing Khan’s people in the torpedoes, tossing the torpedoes into the sun/Jupiter, taking the Vengeance and firing the torpedoes at Khan, or anything you can think of.
It doesn’t help that Peter Weller phones in a scenery chewing performance of his own that reduces his character to yet another of Star Trek’s mad admirals. While it’s hard to make a fully fleshed out villain in a movie already packed with characters, giving Marcus a chance to explain his reasoning and getting him to not sound like an irritated asshole all the time would’ve given him depth and a chance to be seen as a tragic villain. As it is, it’s hard to give a shit when he dies (although you do kind of wind up rooting for him to blow up the Enterprise because of how dumb Kirk is).
Sadly, Khan is stupid too. First of all, he puts his people in a convenient package for anyone seeking to eliminate them, without even bothering to replace the warhead with some inert material. In fact, putting people you are trying to keep alive in torpedoes while being a fugitive on another planet seems like the best way to get them killed. Second, he doesn’t take his alka-seltzer ring bomb (which can devastate a huge underground facility with no problems) and force someone working for Admiral Marcus to use it. That would’ve paralyzed Starfleet, gotten him revenge, and made sure that no one would be on his heels after escaping Earth. Third, he doesn’t beam to bridge of the Vengeance, kill everyone there, vent the atmosphere on the ship, blow his way out of the dock, and take over Earth. I know one of the writers has Tweeted why this couldn’t be done, but like you said, it doesn’t count if it’s not in the movie. Fourth, beaming to a planet you know someone is willing to bomb, in an uninhabited region no less, is not a great way to ensure that a) you survive long enough to be reunited with your crew, b) you are not blown to bits by your own torpedoes, and c) that you luck out and get captured.
At this point, I realize that I sound horrifically negative about this film, so I’ll talk about what I did like. I love the aesthetics of this film, especially the new warp core (that’s actually a real world anti-matter research device). I love the fact that Kirk violates the TNG style Prime Directive to save the primitives. The Vengeance is a great looking ship and seeing it kick the Enterprise’s ass is surprisingly satisfying after decades of impotent combat performances from various Trek shows. I especially love how it’s the best of Ben Sisko and William Adama in one ship – first it punches you in the face with phasers, then it bludgeons you to death with everything else in its arsenal. In fact, I really wish it wasn’t in this film, so it could be the Mirror Universe version of the Abrams Enterprise (and not get wiped out in the reset button ending of Star Trek into Darkness). I also liked that Spock beat Khan by getting him to beam an armed torpedo aboard, although I don’t like how that was followed up (the Vengeance not being vaporized, the extra thirty minutes or so of film after that, Spock not letting the frozen Augments die without any real reason).
Before I switch to criticizing the handling of the heroes, I have one last villain to cover – the Klingons. At no time in the movie did I ever feel like they were a real threat. Marcus mentions that they’ve conquered two planets since the Federation first encountered them – not an impressive track record, even if it’s not taking into account unknown conquests. Then comes the Enterprise violating Klingon territorial boundaries (despite its orders to stop in the Neutral Zone, unless the Neutral Zone is within Qo’nos/Kronos’ solar system) without being detected by anything. The D4 Birds of Prey do make a semi-decent showing until Khan appears and wrecks their shit, and the Klingon makeup itself is great, but having one man steamroll through a few dozen soldiers and three ships doesn’t make them look all that threatening. At that point, you’re wondering why Admiral Marcus is so scared about them and whether or not he’s just paranoid, which probably wasn’t the writers’ intent.
I think Kirk is handled much better in this movie than in the previous one (where he was douchebag most of the time). Yes, his decision to take the Enterprise underwater was stupid, but it’s not like the writers haven’t thought about doing that before (Thirty Days and the initial plan for Starship Down). I’m still not sure why this Kirk and Spock are friends, but at least they have more banter and scenes that prove that they can play off each other well.
Kirk isn’t really that dumb in this movie – sure, he fires Scotty in a moment of anger (although Scotty’s harping about military operations is ironic because Starfleet operates military shuttles) and his decision to capture Khan seems rather abrupt. Sure, he misses the fact that they could probably program the torpedoes to stay in synchronous orbit over the Ketha Province and then send them down in waves after the Enterprise left, but that’s neither here nor there. The real problem is how he handles Khan once they space jump to the Vengeance.
Kirk sees Khan beating the crap out of the Section 31 crew and tells Scotty to shoot Khan when they get to bridge – which is a good, competent decision. What he doesn’t tell Scotty is to set the phaser to kill (which we know Scotty can do, because he sets it to kill (red barrel) when he gets his phaser). Normally, stun would be a good enough option, but this is Khan, the guy who singlehandedly wiped out a ton of Klingons and is leading them to the bridge of a ship that can be operated by one person… and is in weapons range of the badly damaged Enterprise. Stun might not be enough to stop this man and too many people’s lives are in the balance to take that risk. Shooting him with the kill setting (ideally several times, although with Khan’s plot shields, that might not be enough) was the best choice… and Kirk didn’t make the call, meaning he’s indirectly responsible for all the people Khan kills when the Vengeance crashes into San Francisco.
Spock is alright in this movie, aside from screwing over Kirk and being an ass to Uhura. The only real problem with his actions is the fact that he diverted valuable medical and engineering personnel to save the frozen Augments (although there’s a question of how they even had enough time to do it). From a practical standpoint, it’s a waste of resources that could be used to treat injured members of the crew and fix the ship so they can escape. Not only that, but removing the people inside could potentially alert Khan to the fact that the torpedoes have been tampered with, so there’s even less incentive to do it. It seems to me that the writers wanted to have their cake and eat it too – a “dark” film that didn’t require the protagonists to actually dirty their hands, even if what they did made total sense in the context of the film.