1. That stupid 5 second shot of him in the water floating next to the humpback whales. Ok, we get it, you can create amazing special effects. This is pointless, and clearly self-serving.
2. Clark not learning to fly until after he has spent 33 years on Earth, but Zod learning to fly after spending less than a day. Also, Zod learning how to control his powers within the same amount of time. I understand that they need to make sure that Zod can be a legitimate threat to Superman, but really? Zod can do in hours what took Superman YEARS to be able to do?
3. The fight scenes between the Kryptonians went on FAR too long. It started out exhilarating but then just got so boring. Ok, so this super human character is going to punch this other one through an entire cityscape and we will see that he is completely unharmed afterward and then he will retaliate by just punching him in the face into a train yard. And then he will be fine. And so on and so on and so on. Where is the danger or tension in these scenes if we don't see them ever getting hurt!
4. Ok. How many scenes of our pathetic Earth weaponry NOT affecting the Kryptonians do we need? It seems like every time they are fighting we have to have like 1-3 shots per fight scene of puny military officers shooting them with bullets that just bounce off, and then get dispatched as if they are ants. No one in the military would recognize that after they were able to take a missile right to the face and not be phased that maybe they should withdraw their ground troops, lest they suffer countless unnecessary casualties?
5. Kevin Costner dying in the tornado. I hated it. It was so hammy and out of place and just took me right out of the movie. I recognize that this was a visual taken from a comic, but still. Bad.
6. Them just completely disregarding the devastation that had just occurred in Metropolis by ending the movie with a scene involving a guy trying to hit on an intern and offer her tickets to a basketball game. The movie didn't say anything like '1 year later' or whatever to show that a significant amount of time had passed, so I just assumed that it was sometime near to the destruction of Metropolis. Obviously they don't want to end the movie on a sour note, but there wasn't even an explanation as to what happened as far as that goes. Is the city already rebuilt? Had they even started rebuilding it?
When 9/11 happened so much of every day life in New York was shut down for a considerable time following the attacks. This movie portrayed things that make 9/11 look like someone threw a cotton swab at a brickwall and we are supposed to just believe that life at a newspaper would just continue as normal and that people would even be thinking about going out to a basketball game let alone asking a girl out on a date?
Also, how about no one giving any care or acknowledgement to the fact that, obviously, hundreds of thousands of people (if not millions) were probably dying or seriously injured during their fighting. If Superman, Lois Lane, and other named and story-focused characters don't give a shit about something why are we as the audience supposed to?
7. Baby penis.