Having thought long and hard about it, theres some pretty minor/major but simple changes that would greatly improve my enjoyment of the films.
09: Ditch the brewery/have a goddamned CG Warp core to act as a focal point and distract from the random pipes. This is an addition, but during the warp to Vulcan, I'd have had the other ships visible as blips on the HUD viewscreen that you can see drop out of warp, then go dark. Then you have a shot of everyone looking at each other with unease before the dropout to the debris field.
Into Darkness: Swap the Characters of Kirk and Spock whilst keeping their actions the same. Spock breaking the prime directive to save Kirk is a huge deal - with Kirk, the general perception is that he does it 10 times before lunch. This is Spock going against logic to save his friend. The needs of the one over the many. This adds some dimension to the friendship. Kirk responds to Khan's attack on the meeting at first the same way, but after Pike dies Spock gets emotional (he's been in the head of a dying man ffs) and he's the one who rips the unit out of the wall and hulk chucks it at the flyer. If there was a time for him to go nuts, it's after he's felt a person die in his head. This forces Spock to be the one leading the charge after Khan, and Kirk to calm him down and question everything. After all, Kirk's Captaincy was won after proving Spock to be unfit for the job after emotional distress. This solidifies that dynamic, and shows how Kirk has grown as a Captain whilst Spock kept suppressing his emotion as all good Vulcans do, but has let it rise to the surface again in light of recent events. Kirk calms Spock down, but still promises he's gonna grab the son of a bitch that did this - because he's still Kirk, after all.
Personally I'd have liked to not betray Khan, but Spock crunching the numbers and still resentful over Pike has a greater punch to it than Kirk - at least to me, Spock breaking the rules is a bigger deal than Kirk doing it. Then we have a straight up recreation of the WoK bit, because Kirk losing it is less silly looking than Spock doing it. He's brooding and angry, and that Khan scream is very...shrill and petty sounding. Spock looking pissed and muttering "Khan" is an understated take on it, as it stands, that whole scene is borderline parody. Then we have the foot chase through San francisco. I'm not entirely sure how Kirk catches up with Khan, but they have flying hovercar shuttle things, a chase on them before the punch up could be cool. Then we have the punch up. To make things fairer for Kirk, after he takes a couple of hits, he rips open a power conduit and leaves a nasty plasma burn or something on Khan which cripples him enough to make it a fair fight. Uhura manages to send a message over the communicator to Kirk in a lull during the fight - "We need Khan alive, it's the only way to save Spock!" As Khan hears this, he gives a speech about how the only way he can have his revenge is by robbing them of a chance to save Spock. Khan leaps off the barge to his death. Kirk jumps off and manages to grab him and hold onto the edge of the barge. Khan tries to fight him off and tells him the futility of the situation, he can't hold him and he can't hold onto the barge. Kirk says he's right, and lets go - the two fall as Kirk frantically screams to beam them up - seconds before hitting the ground, we follow them through the transport as the transporter pad of the Enterprise appears inches below them and they smash into it. The camera pulls up to reveal a gang of security personnel who all shoot at Khan. Then smash to black - 2 weeks later and Spock is waking up. Khan's super blood yadda yadda. Spock asks why - Kirk says - the needs of the one are sometimes greater than the needs of the many. Or at least that was the excuse Spock gave when he saved his ass on Nibiru, personally, you're my friend. And Uhura would not have spoken to me ever again. Cue speech about who we are, These are the Voyages, ship jumps to warp, the End.