One of my favorite stories is Horton Hears a Who. The protagonist has no particular skills. The only thing that makes him interesting is the sheer magnitude of his goodness. He's the only one who believes and cares about the little people on a speck of dust who are completely helpless against the outside world, and he doesn't stop trying to help them no matter how futile it seems. Superman somehow needs to embody that, except unlike Horton, Superman has so much power that it's hard for his goodness to feel like it means anything. When you barely have to lift a finger to save the day, why does your goodness matter? Superman Returns actually did a decent job of this, with him lifting an entire continent of Kryptonite out the ground and nearly dying in the process. But the magnitude of that leaves you little room to expand in future movies.
If we're doing an intro movie, I think it needs to make his goodness what is at stake. Metropolis needs to be introduced somewhat similar to how Gotham is introduced in Batman Begins: a city that is rotting from within. But whereas Gotham is rotting with corruption, and it takes Batman to inspire fear in that corruption, Metropolis should be rotting in despair, and a feeling that being good doesn't matter. Superman is needed to inspire hope against that despair.
Clark Kent enters, fresh from the farm, having been raised to believe in all the human good things that his adoptive parents taught him - but also reeling from the fact that despite his powers, his dad still died. They mention this in the original film, but it's never really milked for drama. Make it a focal point and combine it with the fact that the world he's entering is bitter and cynical and full of people who aren't exactly bad, but are out to make a quick buck and not worried about helping each other. This further threatens to disillusion Clark. (It's important that the people in the city aren't actually BAD, at least not most of them, so that we can see them as redeemable)
I like the idea of setting the first movie in the past, and end with Clark succeeding at retaining his own faith in humanity and inspiring Metropolis to do the same, but at the same time feeling like he can't interact with humanity on a personal level. It would end kinda like an inverse of The Dark Knight. Clark believes he's more useful as a symbol of power and goodness than as an actual human, leaving us with room for more growth in the next film. (One thing I did like about Superman Returns is that we get a sense of his otherworldliness and Luther's xenophobia being part of his motivation. Set that up to be a major plot point in the second film).
Setting it slightly after World War II is probably the best bet, because otherwise it begs the question "why the hell didn't Superman just END WWII?" The Holocaust and Nukes also let us begin with a real sense that humanity needs to be redeemed.
