Ah you posted while I was replying. That is exactly it. They try to make Superman way too human. Like Ani intimated in the Reeve movies there was no Kal-El. There was Clark Kent who pretended to be a bumbling idiot, who would then put on his superhero costume and occasionally save the day but mostly try to court Lois. In Superman Returns, again there was Clark pining about his lost love and his son. Man of Steel needs a Kal-El. A benevolent yet completely alien entity that mankind recognizes for the legitimate threat that he is.
I will grant you your first two points but it does not really relate to his intelligence later in life unless you want to argue that people who grew up on farms are stupid. Which would just piss me off. Goku though, I can't believe you went there.
The problem is that every superman movie does that, its trite. Then it comes down to does Superman masquerade as Clark Kent or does Clark Kent Masquerade as Superman. Superman is an alien, he is supposed to be an outsider and supposed to be different, yet Bruce Wayne in the Nolan movies feels like more of alien that operates outside of societies norm than Clark Kent does. I always end up comparing the two characters and how they have developed over the years. Particularly how Clark Kent tries so hard to fit in and not draw any undue attention to himself while Bruce Wayne really doesn't give a damn. Perhaps it has more to do with the fact that Bruce Wayne is always Batman but Clark Kent is not Superman which is just weird. I am hoping that Man of Steel is less about a man who just happens to have super powers trying to fit in and explore what it means to be human and more a God among us.
I try to not be too critical of Superman movies, not that there isn't a lot to criticize but it is superman and there hasn't been quality superman movies and the first 2 were good for their time. In the scene your referring to, Clark's reaction had more to do with shock and naivete than anything else.