It feels like, for an origin film, Goyer went too big and too bold.
This whole genetic engineer, codex and terraforming thing seems like something you'd establish in a second, third or even final film. That and the level of destruction on Metropolis and the the threat of Alien invasion.
I dunno, I think it would have been easier to digest if this one focused on the wow and wonder of Superman, like how America and the world would react to him if someone like that came to our world. Instead, it's like Superman sort have had to compete with Zod, the other Kryptonians, the scheme, for his very own, debut film.
I wonder what it would have been like if they dropped the codex/genetic birthing thing and just focused on Superman revealing himself to the world. Then again, there might not be super powered, super being battles which is where I think everyone wanted it to go after the dull Superman Returns.
Still, I think the character would have been more enjoyable if his first appearance wasn't having to turn himself over and dealing with this massive, apocalyptic threat. His origin, Lois Lane tracking him down, gaining America/Earth's acceptance, dealing with the Government, etc. could have been a compelling story/film on it's own.
I admire the scale and enormity, but it would be like if, back in Batman Begins, after we see Bruce become Batman they threw in TDKR's nuclear bomb/doomsday/closed off city plot. Atleast with Begins we got time to breathe with Batman starting out against thugs, the Mob, Falcone and Scarecrow. Poor Supes, as soon as he dons the cape these massive super beings rain down on the earth.
Where does it go from here? Can you have a threat like Lex Luthor? Brainiac? These comic book superhero movies seem to go with the bigger is better approach unfortunately (TDKR is proof of this). I doubt The writers would sit down and want a smaller, more personal story, not when you have a hero who does what he does. But what's left after you save earth from total terraforming, species dominance annihilation and you faced off against your super powered Kryptonian brothers?