Just a few things that would've made it perfect for me;
1. Not just having the Tribble come alive when it needed too. I would've liked something like McCoy looking over Jim's dying body, and then looking at the screen watching the vital's drop to nothing, in the reflection of the screen he notices the tribble is gone. He starts frantically looking for it asking all the nurses but nobody knows...then in all the mayhem he finds the tribble alive and it has already birthed a few others-then the light bulb goes off that his blood could save Kirk. Or something to this effect, it coming alive all of a sudden when it needed to just felt a little short to me.
2. Then maybe just an off-line to continue. As he is putting Kirk into the cryo-tube maybe McCoy could've said something like," Yeah we are putting him in here to save his higher brain functions, prep the guy we just took out for extraction, but I don't know if there is enough time so we need Khan back alive!" I mean who knows if you need to be thawed or not to take viable blood out, but a little more meat on the lines would've made it all the better.
3. "We are safe, we are at warp", here again just a little extra meat on the lines. Like, "We are at warp, he can't catch us. As soon as he speeds up we will just match his velocity and sta ahead." her response could've been something to the effect of, "His ship is too powerful and can make great leaps in speed faster than your helsman can adjust, he'll be able to overtake you no problem.
I think the beauty of the film is that who knows who's plan was thwarted. Did Khan screw up Marcus plans or did Marcus screw up Khan's plans? They way the movie unfolded it seemed they were constantly screwing each others plans up adding more layers to what was going on. The Enterprise and her crew are dropped right in the middle of it all never really knowing whats going on like the audience, except to get their butts home.
Im fine with the ambiguity, just a few extra words on the lines would've great. Infact, the movie reminded me alot of the show Lost which I enjoyed. These guys don't write in a manner that wraps everything up in a neat bow, it allows for some plot holes but I like leaving the theater perpetually asking questions. Makes the beer drinking afterwards fun.
Sorry Roald, that was more than one line!