You could argue Clark was inherently a hero but you can't possibly hope sell Pa Kent as decent father or Clark as a man of conviction. Kent all but scolds at superpowered pre-teen for saving a bus load of his classmates. When said kid asks if he should've let them die, Kent says maybe (Clark masters the art of letting people die by the end of the film). Why would anyone do that? There are ways of emphasizing the need of secrecy without suggesting a sociopathic behavior, every major incarnation of Superman has done it, even the emo Smallville pulled it off. For some reason Man of Steel's Pa Kent sows the seed of doubt in Clark, for no good reason, until A.I. daddy straightens him out.
And that is what happen. Jor-El flatout gives Clark his mission, his gear, and the plans to stop Zod. Had it not been for Jor-El, Clark would've still hitchhiked around America because Pa Kent confused him as a child. If not as a child but then when he suicided via tornado. As the movie shows Clark spends most of his adult life lost and without direction, trying do what is right while appeasing his father's wishes until Jor-El makes Kent role obsolete.
As for Clark developing his person, I agree. He has no personality in the beginning of the film and towards the end Clark to show hints of one. For most of the film someone points in one direction and Clark chases after it. Superman, in his own movie, is the most underdeveloped character in said movie.
I personally dont care that Superman killed Zod but it doesnt make sense in the context of the movie. Zod was the better fighter, dominating the entire fight until Clark put him in a headlock and snapped his head. Zod managed to master his powers in under 30mins were as Clarks struggled with it his entire life. How would Zod lose against Clark unless he wanted to lose?
I could go on:
Why would Clark fly to the other side of the world to stop the Terraforming machine, in the middle of the ocean, when there's a machine in the middle of Metropolis? Since both need to be activate to "terraform" wouldnt it make since for him help the army in Metropolis instead of forcing them to die alone against Zod's army?
Why was Lois taken to Zod's ship other than because Superman has to save her?
Why does Fiora allow the general to destroy Zod's terraforming machine?
How did Clark know he could fly?
Why didnt Zod just look at the family he was trying to melt with his laser I vision?
Why didnt Clark just block his eyes or carry him off into the sky then break his neck?
Why didnt Zod break Clark's neck?
Why did Pa Kent believe Clark couldn't save their dog without everyone figuring out Clark had superpowers? Didnt Pa Kent do virtually the same thing only different being his shoe got caught?
Why is Clark quiet the entire movie?
Why did Clark and Lois make out in the center of Metropolis' ruins? Why were they making out period other than the fact that he's Superman and she's Lois?
Man of Steel's story is painful to watch and is long enough that you start asking questions to shyt you would overlook in shorter films. The transformers movies had the same problems. Pretty to look at but not much there