In terms of story telling, I thought it was pretty weak. I'll probably end up having a bit of a rant, so long post ahead. Also, spoilers.
First of all, we've got that black guy with the sick daughter. What was the point of that? What did that entire sequence accomplish? The only things it did was to establish that Khan's blood could (somehow, it was never properly explained) cure illnesses, and that there was a bombing. None of this needed that family that we never saw again. The "Khan's blood is a magical cure" bit was better explained by the tribble sequence. And as for the bombing? Why did Khan go to all the trouble of having this guy plant the bomb if Khan was going to actually be there in the aftermath (as Kirk saw in the meeting)? Instead of going to all this pointless storytelling, just have Khan sneak in, showing how clever he is. Get's caught, has to fight a few guards (showing how strong he is). Plants the bomb, blows the place up. Establishes his character, shows his intelligence and strength. Sure, it doesn't do the "blood is a cure to whatever disease you might have" thing, but that was explained later in the movie anyway.
If you'd paid attention you'd have noticed that all this ties in with the theme "what would you do for your family".
The first bit was good. Show Kirk saying, "Fuck you" to the rules, and then BAM he gets demoted. Force him to live with the consequences of his arrogance. That was a lot like Kirk from TOS. Making him a commander was also good. But then, as soon as Pike is killed, Starfleet says, "Oh well, we'll just make you a captain again and give you back the Enterprise." WTF is this? What was the point of demoting him in the first place? It would have been far better to have Kirk as Pike's XO (with Spock staying as Enterprise science officer), and then have Pike killed later. That way, Kirk has to EARN his command back instead of Starfleet telling him he might as well just have it back. Maybe have Pike die trying to fix the reactor. That would give Kirk a HUGE motivation to go after Khan.
Again you weren't paying attention. Marcus gave Kirk the Enterprise back, because he thought he could use the hot-head youngster as the perfect fall-guy for his war-plans.
This wouldn't make much sense.
Marcus operates from a position of strength. Why would he sacrifice that position by placing himself in the centre of things?
He tries to use Kirk and the Enterprise to instigate his war with the Klingons.
Which brings me to that whole big fight thing. It's Kirk's movie. He's the one who gets demoted. He's the one in command. and yet, in the big finale, Kirk's on his back and Spock's the one solving the problem. Why? I mentioned before that you could have had Pike die in the reactor (and stay dead). Then you could have had Kirk fighting Khan instead of Spock, and no need for that crappy, "We need him alive" stuff either. It's a movie, Kill the bloody villain.
Who says this is Kirk's movie alone?
Besides, they killed the villain last time, and people where complaining.
Now the keep Khan alive, and people start complaining about that.
And that big ship, Vengeance or whatever... That was the biggest fanwank I;ve ever seen.
It's a warship built for Marcus' planned war against the Klingons. What's so fanwank-y about it?