1. The plot (should there be an origin story?)
I'm pretty sure most people know about Superman's origins, so why repeat it step-for-step? I can see it beginning with the Kents driving at night, when suddenly a meteor-type object crashes into their yard, and then adopting little Kal-El. With possibly a flashback or two of Krypton's destruction. The original Superman dug deep into the origins, probably too deep. We don't need it retold to us when we know it as clear as day.
2. The villains
The original Superman movies were so dry on villains it isn't funny. A message to Warner Bros.: Lex Luthor and General Zod aren't the only villains that Superman has fought. What I would love to see in a potential trilogy for a villain lineup with Brainiac in the first, Darkseid in the second, and Doomsday in the third (with Lex being a sort of behind-the-scenes villain until possibly the third movie).
3. The costume design
First off, loose the trunks. It looks....weird, IMO. And also, give a slight color alteration...maybe take the original design (minus the trunks of course) and make it ever-so-slightly darker?
4. The tone
Warner Bros. has said that Man Of Steel will be as contemporary/real world based as possible, and I honestly don't think that would be successful. Superman is an alien for crying out loud. He can fly, shoot laser beams, freeze breath, etc. That stuff can't happen in real world films, let alone real life. Darker tone is fine IMO, but make it seem like it can fit in our own world? Not possible.
5. The action
Superman has so much potential with his powers that haven't been revealed yet. Just watch a certain episode of Justice League as he beats the crap out of Darkseid. If they relive that scene in the new franchise, I would be thrilled.
6. The actors/developers
I'm honestly beyond thrilled that Chris Nolan put his priceless creative idea(s) into this project. Even though he seems to be stepping out of it now, we'll probably see fruit of his efforts. So far, the actor choices seem good, and Synder looks like a good director (I've only seen some of 300...but what I saw was good). And David S Goyer and Jon Nolan are both involved...enough said.
I can probably think of more later, but this is what I have for now. Any other ideas can be posted below in the usual place. Peace out!