To me, the most suprising "twist" of the movie was that they almost turned Khan into some kind of anti-hero.
From a certain POV he had legitimate reasons for the London bombing and the attack on Starfleet headquarters. I would also point out that Khan had fully cooperated with Kirk and his crew... up until the moment when Kirk ordered Scotty to shoot him. That's the moment when Khan turned on Kirk. Khan probably figured that Kirk must be another Starfleet scumbag just like Admiral Marcus was.
I had a similar thought. For a while I wondered whether they would be going the route of Khan being something of a good guy who got put into a situation he couldn't resolve but through violence and some things in this new universe being fundamentally different from the old one. I thought that the movie might end with Khan and his followers getting their own planet to play on.
To sum up my review in one word: awesome. I liked this better than the first movie (which I thought was great). The dialogue was great, to the point and witty. The story seemed much tighter and more realistic.
I appreciated how they addressed a number of points that bugged people about the first movie, most importantly Kirk's recklessness and that he isn't really ready to be captain but also the coldness with which he condemned Nero and his crew to die. He's on a similar path of revenge in this movie but in the end he (and Spock) let Khan and his followers live.
I thought it was a clever idea to twist the death scene of The Wrath of Khan
around so that Kirk would die. Spock shouting, "Khan!" was perhaps a bit too much, especially since this has become something of a meme, but the scene itself did work and was quite moving, even though I knew that Kirk wouldn't stay dead and I had already figured out how he would be saved.
The character building was also improved in this movie over the last one, I felt. We got two small but insightful scenes with Sulu showing his respect for the captaincy and his subsequent demeanor as acting captain. While Scotty and his sidekick mostly served as comic relief he had a great scene when he objected to the torpedos. Uhura was more fleshed out as well. Kirk, Spock and Uhura really came off as friends. McCoy was great, too - or rather, Karl Urban was at portraying him. The scene where he tries to impress Carol as they're opening the torpedo was hilarious.
I love how diverse this universe is compared to the TOS one. They really go to great lengths to put in aliens as extras and non-white humans for smaller roles. I also loved the design of the Nibiru aliens and that of the Klingons. They looked pretty scary.
Since we didn't get too see that much of Earth in the older shows I'm always thrilled by the looks of futuristic Earth.
Since people complained about it on here I got an extra chuckle out of Scotty's rant about how ridiculous it is to hide a starship under the sea.
And also: OMG! They killed Pike! I really liked him so that saddens me. Would have loved to see more of him.
I love that this movie ends with them going on the first five-year-mission so I expect the next movie to divert from the "villain wants to destroy Earth" scheme. I'm really looking forward to this.
By the way, I saw the movie in 3D and I felt they did a pretty good job with it. There are some nice small effects that are pretty great in 3D.
So, this long-time Trek fan really enjoyed the movie - though now having read some of the negative reviews preceding mine I wonder whether I should feel bad about it.