- Mess in the sense that there's a lot of stuff that clutters the story. Stuff like: Jor-El's idea of saving the planet is recreating it somewhere else, not evacuating it. "We're all dead here", he says... but WHY? Why does he care nothing about the living people of Krypton? And after he dies, Lara could try urging the people to evacuate and save themselves, and she doesn't. She just stands by and watches as Zod gets sent to the Phantom Zone, even though she knows that will enable him to stay alive and fulfill his promise to hunt down her son. She willingly gives in to death, even while aware that her son is in danger. Stuff like that. And Jonathan's death... I know there's a lot of philosophical mumbo jumbo around it, but it doesn't work for me at all. I can't believe that in a film where Superman actually lets his father die, the most controversial element is that he kills the villain.
I can't make you like those parts, but I found them to be quite interesting and moving. Both of Kal-El's fathers were suicidal, which makes sense for them to produce such a morose kid. Jor-El seemed to imply that Krypton was stuck in its ways, and that that was a bad destructive thing. He did not want to spread the oppression of Krypton's genetic classism. That's why it was so important that Kal-El be free born. The hero he gave to Earth is the hero he meant for Krypton, and like his son, he realized he couldn't save both. He kept saying Krypton's time was past in one way or other. He may not have explicitly connected the two ideas of not wanting to continue Krypton, but the implication is very strong. An explicit connection may have helped change the platitude into something practical though for some.
Johnathan did exactly what it looked like. He told his son not to save him. Consider the fact that what was on the screen was exactly what happened. Johnathan Kent said maybe there was nothing else he could do as a Father, then he sent his fast strong son back to the bridge while he went to save a dog, and when in trouble, he looked his son in the eye and said don't save me. That's not a man who intends to live, that's a person who wants to drive a point home, and Clark got that point as he explains by the gravesite. It is not outside of Pa Kent's character to die for what he believes in, and it's actually the strongest lesson he could give to Clark, so it makes sense that he would.
Now we can ask why didn't Clark just disobey his father, but I think the film paints a compelling picture of why he would let his father die if he asked, as his father had spent the last ten years telling him to let people die, and allowing him to experience negative consequences when he saved them.
The film doesn't really suggest that Lara knew what would happen to the Phantom Zone prisoners if the planet was destroyed, or that she had any power to do anything about it. It'd be nice if they had addressed it in someway, but I think it could go either way, and it'd have been a bigger flaw, to me, to have any more storlines on Krypton.
- Jor-El's hamminess: the way he says stuff like "That's madness!", or the way he talks to Zod in the scout ship... it's a little too big for my taste. He went a little too far with the operatic-ness of his performance, imo.
- Hamilton's not the most important character, but he serves well as a mentor of sorts, something Superman could need later on. Schiff's a cool actor to have around, so to waste him like that... His death didn't even have much meaning. Hardy's did, but his didn't. It's not a big deal, but it's a bummer that we won't get Schiff back, that's all.
I totally agree with these, I see these as flaws in the film. I think another generic scientist would have fit here better than someone who actually plays a significant role in the mythos.