I think the thing that bothered me the most (but don't misunderstand me, I enjoyed the movie immensely) is the fact that if he is so bloody high-minded and noble, why didn't he feel one iota of guilt about haring off to the other side of the galaxy for five years, leaving his Arctic fortress with its vast repository of knowledge completely and totally unprotected from the depredations of any insane evil genius with a helicopter? And why were there no safeguards in place inherent within the big crystal house, so that Jor'el's image would not mistake Lex Luthor for his son, and say, "Here is all the literature and scientific knowledge from a kajillion worlds. Whaddaya wanna know?" Seems like Krypton would have at least one white-hat who could figure out a way to keep someone from just strolling in and downloading at leisure.
That is all.