Personally, I'd rather see a change in how the Superman movies are made. While you all use the word "Dark," I don't see a transition as needing to be dark, per say. Right now, we've got a happy-go-lucky Superman thing going on. Superman flies into the everyday world, and yeah, there's a villain, and yeah, his/Clark Kent's life might not be perfect, but all-in-all, the people are superficial caricatures of human kind. It's campy. The movies are far too campy. They get too bent on making Clark Kent a "mild-mannered" reporter, and it's ridiculous, because these characters have evolved. Kent is a hot-shot reporter who doesn't have the fame of Lois Lane, but he's almost anything but mild-mannered now.
Luthor is much more than an evil corporate villain. He's a slick business man, but not inherently evil. He sees himself as all that's good of mankind, the pinnacle of evolution. All of a sudden, this...alien...comes in and steals that away from him. He thinks that if Superman were to get out of the way, he could cure cancer, that's his problem. He doesn't believe he's evil, he thinks he's working to stop Superman for the good of the world.
Then you've got Lois. They need to jump past the point where she doesn't know that Clark Kent and Superman are one of the same. Get to the point where he's courting her, or even when they're married. The point that she's at now is intolerable, really. Super Baby needs the boot, too, for a long time, at least.
Superman isn't dark. No, Superman doesn't walk the line of hero and villain, he doesn't beat confessions out of people, and he doesn't question his morals, ever. However, Superman can be serious, rather than the camp we've seen. Superman is about sacrifice. Here we have a man with "Super" powers, right? He doesn't have to be Superman, he doesn't have to save the world, he doesn't need to. He's got a loving family, a great job, and a romantic interest, but he does do it, anyways. He's Superman because he wants to save people, but it costs him. It costs him the best stories, it costs him time with Lois, it makes him enemies, and the one tricky part is if the villains exist solely because he does. They need to express that better. Why does Superman fight? Why does he save the day? Why does he sacrifice a normal life, children, his job, and everything to fight people and enemies that probably wouldn't be there if he weren't? That's the inner turmoil we need to see in a Superman movie, really, and I know it's shown a little bit, but not really. It's been pondered, that's all, never truly considered.
Also, we need a real villain, Brainiac or Metallo are my picks, but there's a few others that could work to begin. Honestly, I prefer Brainiac, someone that would have been around regardless of Superman, to show why he is needed.