The first hour or so was pretty good. The second half on the other hand was a mess. Ripping off Wrath of Khan was extremely annoying. I dont mean using Khan. I don't mind that part. I think Cumberbatch's performance was the best thing about the new movie. I mean the fake Kirk "death" scene where they actually took the words line for line right out of Wrath of Khan. Even the shots were the same. The only difference was Kirk and Spock traded places. Then Spock yelling "Khan!!" was laughable. Seriously. I saw it in theatres and a lot of people laughed at that part. I have a feeling that death scene was not supposed to be funny. If they had left Kirk dead it would have been better. At least when Wrath of Khan ended Spock was still dead and no one thought he would be coming back. In this movie Kirk was "dead" for five minutes.
My only other complaint was that there was too much action and too little plot and character development. Really take the action out and the movie is about the length of one episode without commercials (45 minutes). It was really well done action and the special effects were awesome but really, if the plot is thin and I dont care about the characters in the action it looses its effect. It just becomes dull eye candy with little to no re-watch value.
It was also funny that the supposed villain, Khan, was justified with most of his actions. The Admiral he skull crushed seemed to be the real villain to me.
Q, The Prophets, Pah-wraiths, Changelings, the Xindi (3 of the species anyway), the crystalline entity, cytoplasmic life form, species 8472. Those are the ones I can think of off hand. All in the sequel series.