They seem to tone down the weaknesses for him a bit due to not being as strong as the guy they were usually very effective on: PC Superman.
Seriously, between him, Post Crisis Superman, and Nu Superman, HE was always the most effected by the stuff than the others. Why? He was so damn powerful is why and DC knew that. So they brought in two weaknesses that really hurt him: Kryptonite and Magic. To try and even it out a bit. Post Crisis Superman was nowhere near as strong as PC Superman so they toned down the weakness to magic and kryptonite quite a bit as he wasn't as op'd as PC Supes. They may end up doing similar to Nu Superman, depending on how powerful he gets.