1. Pa Kent being a waffling pussy about the conflict between Clark's "reveal" and yet trying to teach him to be responsible with his identity and powers *HOWEVER* his concern was probably with trying to keep a godling in check who could kill someone at will;
2. Insane amount of collateral damage by Supes;
3. No sense of developing a real connection with humans as those he's sworn to guide and protect (see above);
4. Zod, Faora and the others being 25-30 years older and looking/acting almost identical when they reach Earth (though the same issue happened in Superman II, but In MoS the villains spent far less time in the Phantom Zone);
5. Too much content variety in the same film - the problem, though, is if there was less action it would have been boring; any more, and it would have nothing to stand on (plot was light as it was, but sufficient for an action film, IMO). The irony to me is that Snyder did what many on these and other forums suggested and did a very sparse background with emphasis on Krypton - much more science fiction-oriented, which I thought was a nice twist on the retelling of Krypton, even with the Avatar elements;
6. Superman/Lois Lane's relationship developing faster than Thor and Jane Foster's;
7. Killing Zod: the biggest problem I had in this case was not him actually killing Zod, but Snyder - and Goyer - trying to make Zod a sympathetic character up to the very end. Superman had completely ended Zod's purpose for existing, but rather than have him threaten to kill Superman or every human being one by one, he bemoaned the whole issue of not having any purpose due to no longer having a Krypton to defend. Zod should have been shown to be what he was: deterministic, mad (with power), and willing to kill every human and Superman or die trying. In this way he would have been much more like Doomsday: a nearly unstoppable threat that only death could halt. By having him kill Zod, they had Superman cross into the gray area of morality, and honestly have nowhere else to go with him.