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In the movie, he was clearly anguished at the time, but we don't see any ongoing remorse (about Zod or any of the presumable thousands of Metropolis bystanders). Maybe it took place between scenes, but it would have improved the movie to show some of it. They certainly could have have traded out some of the miscellaneous property destruction scenes.
I don't agree with Clark self-exiling in this circumstance - it does no one any good and it's just running away. No, we don't see ongoing remorse afterwards - it's the end of the movie. We've seen the climax, and it makes no sense to continue the movie for very long after that. It would have less impact. They just close it up with a tag (which I'd say very soon after the battle) - an upbeat one, even. Hopefully we will see some guilt in the sequel - not that I think he should feel guilty (I think he did the best he could, the best that could be done), but I think it's in character for him to agonize a bit over Zod's death. I certainly don't think he should self-flagellate over the deaths in Metropolis/Smallville. Mourn for them, absolutely - blame himself, no.

I mean, I wouldn't have minded some of the building-falling being replaced with plot/character-driven material - I'd have loved it. But we didn't need significant time after the climax - that just isn't the pacing I'd prefer.

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Now that I think about it, such a transition could have also covered his decision to operate openly. Yes, he had decided to expose himself to appease Zod, but that's different from being an everyday superhero, throwing the fact of alien existence into everyone's faces on a regular basis.
I disagree with this entirely. That makes being a hero (openly) being about being under the judgement of the public eye. It's negative. It should be positive - about embracing what he's always wanted to be. It should be about choosing his destiny himself, as his birth parents wanted for him. That is the theme to me in the movie - that Clark always wanted to be a hero, to make a difference, but would never allow himself to live that way. He'd move on every time he did, because he thought the world wasn't ready or he wouldn't be accepted - letting society dictate his destiny. Now he he takes a stand and claims his own destiny - the one he wants.

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but I think it's important to recognize that his motivation for secrecy was not Clark's personal safety -- I think we're projecting that from L&C. Instead, this Jonathan believed he was protecting the world from information it was not ready to handle. Letting a few die for the greater good is an understandable position, though not something we generally associate with Superman.
I disagree with this. It was about Clark's safety to me - because of the way the world might react, it would make his son unsafe. And, frankly, if Jonathan is taking it upon himself to decide what the world is ready for, that is Doctor-level (Doctor Who) arrogance. I mean, wow! What greater good is accomplished by preventing people from learning a great truth? He doesn't say anything about society collapsing or rampant murder, does he? It's all in terms of Clark.

Speaking of this bit - I didn't think Mrs. Ross seemed scared or rejecting. She was very positive and attributing Clark's uniqueness to God and treating it like a good thing. She seemed more awed than fearful to me. That has it own potential set of Very Bad Consequences, but she didn't seem ready to start a chapter of the Friends of Humanity.