The main theme of the movie is The Needs of the Many.
Every character has to make a decision between what is good for one person (or a dozen, or a thousand, or more) and what they consider to be "the greater good".
- For Jor-El and Lara, their son Kal-El is the hope of Krypton's future, a potential bridge between two worlds, and a chance for their people to break free of the cultural and genetic programming that turned Zod into a monster and doomed their planet.
- For Zod, Krypton was the greater good. He'd been programmed (genetically and culturally) to protect Krypton at all costs, whether the cost was the Kryptonian Council or his friend Jor-El or a planet of billions. Nothing was more important to him.
- For the people of Earth, represented by General Swanwick and Colonel Hardy (and Perry White, to a lesser extent), protecting Earth is the greater good. They're all willing to sacrifice Superman for that; but would they sacrifice Lois Lane when asked, "one of their own"? Once they decide that Superman is on their side, then they're willing to work with him to protect the Earth, and all of their lives are expendable in this.
- Lois Lane, of course, is a Pulitzer Prize-winning journalist who is willing to literally put her life on the line for a story, and she has a story: An alien walks the Earth. She knows the story is going to come out, and she wants to be the one who breaks it. But when she hears what Clark's parents sacrificed to keep him safe, she has to decide whether it's worth it, finally being the one to expose his secret.
- Jonathan Kent tried to teach his son from an early age that the world wasn't ready to know what he can do since he knew that his son was not ready to use his powers openly and deal with the consequences (geopolitical, religious, scientific etc.) it would have. This is not easy for Jonathan such as when his son asks if he was supposed to let a schoolbus of children die to keep the secret and Jonathan can only respond "Maybe". Bear in mind that Jonathan was willing to sacrifice his own life, as well. He did it for Clark and the world, whose needs he believed to be greater than Jonathan's own needs.
- The hardest decisions were made by Clark himself. He still helped people, but every time he did, he tried to keep himself hidden, as his father said. If helping people meant exposing his identity, then he found himself a new one. When he had to destroy the World Engine to save Earth, he didn't hesitate to place his life on the line. And when he literally held Zod's life in his hands and knew that Zod would "never" stop trying to make the humans extinct, one by one if he had to, then Clark sacrificed the last living link to his people (not to mention his own soul) to save Earth one more time. It's the hardest decision we've seen him make, and he did it for the greater good.
Clark's smile is a visual storytelling element.
We don't see Clark smile in this movie...is the accepted wisdom. In reality, he smiles quite a bit in the film. The first time we see Clark smile is when he learns his real name, Kal-El, from Jor-El. It's a tentative smile as he's taking his first steps towards learning who he is, what his ultimate identity and purpose is. The next smile we see is much bigger as he flies for the first time. He's spent his whole life hiding who he is and what he can do, but as he dons clothing from his own world and pushes his limits, he feels like "himself" for the first time in his life. After this scene, we see him smiling much more often, usually either around Lois Lane or Martha Kent. And, of course, the last scene of the movie is Clark with a huge grin on his face, his origin story complete.