First, disregard anything Geoff Johns does with Superman. He tries, I love a lot of his other work, and he seems like a great guy, but Johns really does not get Superman. The Apokolips thing and the solar flare "power" being only two examples why. The Apokolips thing could have been cool if it had been done in a totally different way.
As for weaknesses in general, Kryptonite is fine with me. It's sorta unique now, no one else still has a silly dues ex machina flaw anymore. But writers make it either paralyze him or depower him. All it's supposed to do is inflict crippling pain. More potent and/or larger chunks should have a more powerful effect but it's something Clark should be able to push through and get around most of the time. And I never warmed up to the idea of multiple colors existing. There should be green, and that's it. An artificial, lab-created red kryptonite or something? I can deal with that now and then, I think that's great, but green should be the only "real" kryptonite there is.
The magic weakness always seems blown out of proportion to me. There's no reason for Clark to be more susceptible to magic than anyone else.....it's just that he's not especially resistant to it like he is most things. A weak blast from some two-bit wizard should maybe sting a little bit but it's not going to slow him down while a powerful blast from a real arcanist is going to knock him on his ass....just like it would anyone else. Magic is dangerous for Clark, but it's not an automatic "I Win" button for the villain, either.
I'm on the fence about the red sun thing. I don't like it when it's treated like an "off" switch for Clark. A power drain? Okay.....I can see that I suppose, though I'd think that all it would do is prevent Clark from replenishing his solar reserves (and we know he's not gonna run out of juice quickly so its not much advantage in combat). But I don't like the idea of it just instantly taking all of Clark's powers away, and I definitely dislike it when it's treated like a common technology any smuck can get a hold of. That's not just colored light, that's cosmic radiation from a completely different galaxy. It's not gonna be easily replicated.
And I don't think Clark needs any more weaknesses than those.
Well, his enhanced senses can be used against him, but DC seems to usually forget about that.