One thing I hope the new 52 does is put a bit more thought into Superman's weaknesses:
Kryptonite: Great tool to use if done properly and not going to the extremes of causing him crippling pain when simply around an ounce of it. Personally I think the best explanation for why Kryptonite affects him so much is by going with John Byrne's idea that Kryptonians had a physical connection to their world (perhaps combining that with the idea that for awhile they were galactic conquerors and as punishment the Guardians changed their physiology so that they couldn't leave Krypton again) and while Jor-El eventually created the serum that allowed Kal-El and Kara to leave Krypton with no ill effect, their is still a lingering connection and as a result being near pieces of their homeworld re-establishes that connection. As those pieces are now radioactive, they cause the harm that is normally associated with kryptonite, like poison. But it shouldn't knock Superman on his ass right from the start. Instead its a gradual effect that slowly diminishes his abilities and causes him pain, but he can still fight through it if needed (modern examples of this way of using it would be when Superman fought a Darkseid mind-controlled Supergirl in the pits of Apokolips while wearing a kryptonite ring.....as Kara was not used to the harmful effects of kryptonite.....or while fighting All-American Boy in Superman/Batman). As for the other colors, the only one that shouldn't exist is gold. Too much of a cope out to simply remove their powers in an instant (even if the modern version only lasted a few minutes). It made sense, somewhat, for the New Krypton stuff but shouldn't be brought back in the new 52.
Once we get that established need to showcase how kryptonite can be used against him outside of as a chunk of rock. For instance, get rid of the idea that punching him with it makes him vulnerable to a normal strike (say, Batman or Lex hitting him with a kryptonite ring on their hand). That just doesn't make any sense. But it would be acceptable that a bullet of kryptonite, with the velocity and force it would be hitting his body coupled with the affects of the radiation, would penetrate his skin. Also, kryptonite-based energy attacks would burn his skin like a radiation burn. That way a villain, like Metallo, can't just be in possession of a chunk of kryptonite and hold it up to him (though in Metallo's case keeping the kryptonite exposed would gradually weaken Supes even as his strong attacks stagger him). They would need to do something extra with it, especially if they only had a small quantity of the stuff.
Red Sunlight: Again, something that has been used correctly at times and then not. The only time I've really thought this concept was used correctly was in the OYL storyline in Supergirl when she and Power Girl were acting as Nightwing and Flamebird in Kandor. In that storyline the two retained their abilities even though Kandor had a red sun because of the solar energy stored in their bodies. However, they couldn't replenish those supplies in a red sun environment. So if they used their abilities too much rather than the mechanical suits they wore (such as when Supergirl used heat vision and Power Girl criticized her about it) they would burn out their stored solar energy. That seems like the best use of this weakness because it fits with the idea of cells storing energy. It wouldn't all be released instantly every second because cells would constantly be getting destroyed and replenished at an alarming rate. Basically Superman would always be fluctuating between normal and super in fractions of a second. That doesn't really work. So keep with the idea that his cells store that energy for awhile and showcase him getting gradually weaker (well, moving towards normal) the longer he's active in a red sun environment. If there long enough his body would naturally run through its stores because energy can't be held indefinitely, just the simple acts of being alive and moving will deplete them, but at least it doesn't instantly make Superman un-super.
Magic: No change to this, think the writers have done it correctly. He's stronger than normal humans when it comes to direct magical attacks (like a bolt of lightning) but has no natural resistances to magical weapons (whether they be held, swords, or natural, claws).
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