So according to many sources, the Nolans will be introducing some sort of “major twist on the Superman legend.” First off, I recommend that they read my article: http://thehumanscorch.wordpress.com/2009/12/20/how-to-make-a-proper-superhero-movie/
…because this definitely falls in under the “know which things to tweak” zone.
So let’s speculate as to what this could be:
1. A change in Superman’s ethnicity.
This would be the most bold, and the most stupid as it would quickly be rejected, and totally take people out of the movie before it even opens.
2. A change in the reason that Krypton explodes. 
This could actually be fun, interesting, and not offensive if done right.
3. A change in Jor-El’s character.
Instead of being an altruistic visionary scientist, maybe they’ll make him be someone else. Meh.
4. Something about the Kents that we never knew.
This could be fun as long as they don’t confuse “dark” with “good.” Part of the whole foundation of Superman was that Clark was raised by a certain kind of parents, and that’s where he gets his values from. If they change that, then…We already have enough heroes motivated by tragedy and guilt.
5. Changing some of his powers from biological to technological.
This is kind of the opposite of the Spider-Man twist…changing his web shooters from mechanical(which always showcased Peter’s genius, and created new opportunities for jeopardy for the character) to organic(which I personally loved and always thought made the most sense). But there was quite an uproar over Spider-Man. I think it would be too jarring to find out that there’s a jet pack under the cape.
6. A change in the way Kryptonite works…or even exists.
Nolan strikes me like someone who would have an extreme distaste for the concept of Kryptonite. So he might eliminate it or change what it does. Although the idea of Kryptonite being Nolanized(i.e. “real world grounded”) could be even sillier.
7. A major change in the supporting cast.
Any of the above twists that would apply to Lois, Jimmy, or Perry.
….feel free to weigh in with your own ideas.
Hmmm, the way I see it if any changes are to be done they need to be fairly innocuous. The problem with messing with Supes is that pretty much everyone knows his mythos already. I'm not talking comic book folks, I'm talking middle America and the like. A major change to the mythos could spell disaster for the property.
I'm of the opinion that you do more with less. If Nolan doesn't like a certain aspect of the Superman mythos don't change it, just don't include it.
"The problem with messing with Supes is that pretty much everyone knows his mythos already. I’m not talking comic book folks, I’m talking middle America and the like. A major change to the mythos could spell disaster for the property.
I’m of the opinion that you do more with less. If Nolan doesn’t like a certain aspect of the Superman mythos don’t change it, just don’t include it."
All of that is very well said. He's too well established as a character to tweak him too hard. People all over the world know what Kryptonite is. 🙂
Perhaps the twist will be one inspired from the Smallville series. I have really enjoyed the way it was done. Some things were odd and hard to digest but overall a good series. If they do a kryptonite thing it may be the introduction of a new color and effect.