So here are my thoughts on Star Trek Into Darkness. Spoilers. Like, big ones.
I really liked everything about it...except the script. The acting was good. It looked pretty in IMAX. Nice action. A little character growth for just about everybody, even secondary characters like Uhura. But that script...no. Was it written by a twelve year old? I'm going to ignore the plot holes and try to just deal with the major story elements and themes.
Let's start with the title. This was not a very dark movie. Nobody really had to confront and overcome their inner demons. Wrath of Khan was darker than this and I've been through BSG since then. So if you want to go dark, fine. Let's see how that looks in this universe. But don't tease. Maybe they were trying to show the dark side of the federation, and what happens when they stray from their morals and principals. But TNG and DS9 both did it better. The Undiscovered Country did it better. The entire run of Voyager is pretty much an object lesson in how sticking to your ethics puts you at a disadvantage. I think they basically proved that Star Trek is not made to be dark.
Were there any real "twists?" Bones plays with injecting Khan's blood into a dead tribble and I think everybody in the theater groaned and said "gee, I wonder if that will come in useful?" The last 20 minutes of the movie are obvious from the moment you realize Kirk is going into the core. Reversing Kirk's and Spock's lines through the glass door was obvious. I was reciting them the moment Spock left the bridge. And having Spock scream "KHAAAAN!!!" Tacked on? Or shoehorned in? Discuss amongst yourselves. Was anybody surprised that Spock used the torpedoes to blow him up? Anyone? When he tells Khan that they are his torpedoes I rolled my eyes because he almost came out and said "but I never said they had your people in them!" Using what Khan wants to defeat him is nice, except that I would like to think Khan's superior intellect would have figured out that dodge. Maybe it is nostalgia, but I prefer Shatner using Khan's arrogance and inexperience in 3d combat to defeat him.
Speaking of which, lets talk about Khan. The entire way that "secret" was handled by the production crew was just awful. Either tell us you are using Khan in a (sorta) clever new way or come up with a new villain. And be aware that anybody who even slightly wants to know, will know before they enter the theater. And if you are going to try to be coy about it, at least let Cumberbatch use his whole name. He's an arrogant SOB. He doesn't say "I'm Khan, glad to meet ya." He draws himself up, thrusts out his chest and as the camera slowly zooms in on his face he says "My name is Khan Noonien Singh." Also, a little about eugenics might be nice. Otherwise his whole presence is just fan service. Which it was. I can only imagine a non-fan being in the movie saying "what now? There were superhumans 300 years ago and the Federation froze them? Can we get a line or two of exposition here?" In fact, anybody who has only seen the two Abrams movies probably thinks the Federation is a pretty corrupt, stupid organization. They are the real villain of this movie.
Overall, it just seemed that after four years they could have come up with a better script. Close a few plot holes. But it seems that the script existed to serve the action and not the other way around. It's not Michael Bay or Roland Emmerich bad, and people don't act as stupidly as they do in Prometheus, but it has aspirations in that direction.