Major spoilers follow. While I won't be getting into how the movie ends, I'll still be getting into the backstory of Kal-El's origins as exposited by the film, and talk about various revelations made in the film, all of which may differ significantly from the canonical story you grew up with.
If the story line of the movie seems weak in points, realize that the story line was never very strong. Sometimes making a story more realistic only makes the weaknesses more obvious. The traditional explanation of Superman's powers is so ludicrous, scientifically speaking, that it makes the most other comic book superheroes plausible by comparison. It's a difficult story to "update" in the sense of lending it more plausibility in terms of modern scientific understanding.
What destroyed Krypton? Tired of the old idea that Jor-El was the one scientist smart enough (in a planet full of technologically advanced aliens) to figure out Krypton's impending doom, in this retelling Krypton's doom is obvious. The planet is falling apart around them. What isn't common knowledge is that Krypton is so close to destruction there's no point in even evacuating it. Jor-El's advanced mind grasps this. Jor-El was working on his documentary A Belated Truth after selling his tv channel to General al je-Zod for stacks of Kryptonian cash.
Here is where we get our first politically charged message--in one of the first storyline changes: Planet Krypton is destroyed not from natural causes but from a short-sighted energy policy. Nice bone thrown to the environmental activists. But it gets even weirder... The whole planet appears to be a collectivist, statist regime run by a global Supreme Court oligarchy, but in spite of not being burdened by a Senate or other republican sort of legislature, the planet was doomed because, as General Zod puts it, they were too deliberative to take action sooner.
|Captain Planet Gore|
Because of a combination of their problems with population genetics and living resources, Krypton's Supreme Leaders have inexplicably given up on a previously stellar (no pun intended) colonization effort. Miraculous "world engine" technology makes planets inhabitable in very short order, and yet Kryptonians huddle together on their own dying planet, in spite of being able to travel to other solar systems in minutes and terraform planets in a matter of weeks. What is the big hold-up on saving Krypton? Apparently being too deliberative and not having a powerful executive branch that can take decisive action. I guess they needed to narrow down their Supreme Court to one powerful Reformer. Zod thinks so.
Enter General Zod. He is a man of action. He is a military man, exactly as his name implies. Funny thing: There is no mention of any other aliens that Krypton is at war with. Why do they need an obviously very powerful military? Zod is not trained for war against other sentient races but against his own. He is homeland security for Krypton. If there is a Waco on Krypton, or people start sending each other emails about a Bill of Rights, Zod is Janet Reno and the ATF rolled into one. He apparently quells dissent from Kryptonians who don't realize that libertarianism is a threat to the collectivist state.
Zod is a product of the collectivist state; he says so himself he was specifically bred and raised to perpetuate it. What makes Zod different from his fellow socialists? Just as Thomas Friedman and Luis Seidman are annoyed with legislative impediments to a fast-acting empowered and enabled national power, Zod is sick of checks and balances. But that isn't all. He seems to be a big fan of a brand of eugenics (which it seems Krypton has already implemented) that favors particular hereditary lines. It seems that the screenwriters try to distinguish Zod by the very Darwinian ideas that Hitler latched onto, popular among the scientists in both Europe and America in the 1920s and 1930s. One member of Zod's little personality cult gives a sermon on the superior amorality of these evolutionary beliefs. A little inconsistent as Zod does believe in principles and in a Highest Good, an Ultimate Concern -- it just has to do nothing to do with anything outside a Marxist materialism.
To me it seems that the screenwriters hope to communicate that Zod is somehow to the political right of his collectivist statist peers. After all, it's claimed that even though Hitler was a collectivist and a statist, the fact that he promoted nationalism and racism (and sought complete control of private corporations instead of eliminating them altogether) placed him squarely on the Right. The ruling oligarchy is apparently composed of good socialist statists (and still somehow manages to ruin the planet) while Zod is the kind of totalitarian collectivist you gotta watch out for.
The ruling oligarchy not only condemns their society's destruction by the total dismantlement of their space program, but as a final political act, ensures that the only Kryptonians that survive the apocalypse they all know is coming are Krypton's most dangerous criminals. Yes, the great minds of Krypton might have survived, but instead, it is Zod's death cult alone whose survival was made possible. It's a very liberal penal system. And I can tell you right now, their "somatic reconditioning" program (Clockwork Orange?) doesn't work that well. Maybe it requires a few centuries.
There are also a lot of messages against xenophobia. People are afraid of what they don't understand, especially when what they don't understand is capable of single-handedly taking over a country, assassinating a President, etc. It's ok though, Clark grew up here, just like Timothy McVeigh and Nidal Malik Hasan. Everything's cool. Clark may be an extraterrestrial capable of destroying humanity if he were so inclined, replacing our government if he didn't agree with it, but he really poses no threat to national security. Yes, world, be afraid of America since it is too powerful for its own good, but don't fear Superman, who can invade the capital of any political body at will. Superman, in every sense of the word, constitutes a sovereign state in his own person. He is truly not subject to any law other than his own.
Clark is, he says in the film, "as American as it gets." Yet, unlike the recent Captain America, Superman no longer stands for "the American Way." After all, we don't want to make the same mistakes that Krypton did with its overly deliberative "one party system." As with Obama, America is special to Clark only because he happened to grow up here, not because of anything special about this especially xenophobic melting pot.
The messages about religion are mixed. At one point, Clark consults a clergyman (helpful clergy always wears a clerical collar so you don't think that evangelicals are anything but dangerous) and gets some positive advice. There is even a picture of Jesus in the stained glass window in the background. Earlier in the film, however, Jonathan Kent tries to hold back his amusement at a local heartland resident who naively believes that God has worked a miracle. No, it is no miracle. It's science. Growing up on a different planet just allows you to levitate at will on this planet and generally defy as many laws of physics as one might wish.
Clark is here for a purpose, Jonathan believes, but one that has to do with Clark's biological father, not a spiritual father. (Jonathan doesn't for a moment consider that Clark might've been sent by a Zod rather than a Jor-El.) It is not God's Son who will save the Earth but the son of Jor-El. Now, setting aside the messianic qualities that this movie inherits from the original franchise, the movie drives this point home in an overt way. At the moment Krypton's only begotten son (the only natural born son of Krypton) is given a message by his heavenly/celestial father that he can save all the people of Earth, before taking off to do just that, he adopts a pose that we don't see in any other part of the movie. He adopts a clearly crucifix pose, as he steels himself to potentially sacrifice his safety for all humanity.
Earth doesn't need spiritual help, it just needs leadership that inspires Hope. Why does the 'S' mean "Hope" and not freedom? At the beginning of the film, Jor-El seems to be preaching "freedom" (which is denounced as "heresy") and toward the end talks about "hope" as the belief that we can all be agents of change. The god-like alien will apparently show everyone how to "be the change." Hope and change. Why does that sound familiar? This is in stark contrast to Captain America, who quips at the mention that Thor is a god, "There is a God, ma'am, but I'm pretty sure he doesn't dress like that." Amen, Captain America. God doesn't wear a cape. And, unlike Jamie Foxx, I don't believe he wraps himself in the trappings and title of "President" either. Social Democrats and Marxists gravitate to a Messiah whose kingdom is "of this earth" which is the opposite of what Christ claimed.
In spite of all these messages, I would rate this only a 5.5 on the Lib-o-meter. Obviously written by liberals, but they are holding back so much that they probably think they were being entirely apolitical. No plugs for marriage redefinition, no overt reference to Superman being an illegal alien, no mention of the word "diversity" or PSAs from Superman to spread the wealth. No references to capitalism or corporations having wrecked Krypton. (Although, look for Lex Luthor to represent Corporate America in the next installment; there were several "LexCorp" trucks in this movie.) Unlike Superman IV, no preaching disarmament. Yes, they were holding back this time; yet, unlike Dark Knight Rises, this does lean to the Left.