Lets take them one by one..
First, I felt the film did a nice job of showcasing how Clark was born with his instincts and morality. He was not told how to act and feel by his parents as many have claimed. As a 10-12-year old, we see him save his classmates from drowning after the bus tumbles into the water. The mother of one of the kids he rescued is having coffee at the Kent house and explains that "this is not the first time Clark has done something like this". Later in his 20's, we have a scene where he saves an entire plant of people. He saves Lois multiple times and others throughout the film. At the very end of the film we see a young Clark playing in the yard with a "red cape". If this isn't supposed to signify that he was born to be Superman then I don't know what would.
Pa Kent is certainly there for guidance. Clark wants his life to "mean something" as he explains in a car ride and he tells his father earlier that he couldn't just let those kids die. Pa Kent is not against this idea that Clark can change the world, he simply wants him to wait until the time is right. He does not tell Clark not to save mankind overall, just that they are not ready to witness what Clark can do. Clark will know when the time is right. The tornado scene was hokey and contrived but that would only be a minor gripe for me.
Jor-El is definitely not telling Kal what to do so much as he is offering reassurance. Kal already wants to be a "Superman" type figure well before Kal establishes the significance of his landing. I had no issue with any of this. Critics have said that Superman shouldn't have doubt but I don't mind this take on it. He is still developing as Superman and as a "person" on earth
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.
RE: Zod's death. Zod says "This ends with one of us dead". Zod was already banished to the phantom zone and came back. Zod will always keep coming back. Superman never showed that he could strong man Zod away from anything. Superman could not simply "lift him up and away from those in danger" as others have stated. This was his first real fight and Zod explained how he was a born warrior who was adapting easier to the elements in terms of fighting skills. Zod was the stronger being in this fight. This as fact, he was stronger than Superman at that point in time. Superman was still developing his skillset. People have taken issue with how he dealt with Zod but Zod cannot be imprisoned. It is better in my view that it ended this way than for Zod to be banished and then come back and kill even more innocents. That is a failure in the comics because Superman is often left with blood of innocents on his hands.
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
' and I'm like 
He destroyed half of Metropolis fighting Zod. No mention of a body count? That had to be in the thousands
