Let’s say you’re writing a Superman story and you want to make it seem like Superman is in danger. One of the most persistent complaints about the character is that “He’s too powerful!” and “He can do anything!” Basically, the idea here is that he has no weaknesses, so it’s unbelievable that he could be threatened. The thing is though, Superman has weaknesses. Hell, everybody knows he has at least one weakness. His most famous weakness is so well known that we actually use it as a term for weaknesses that anyone has. Next to saying that something is your “Achilles Heel”, saying something is your “kryptonite” is probably the most well known way of describing a weakness without just using the word “weakness”.
But if you have to work kryptonite into every story, you end up repeating yourself every month, which means things grow stale. It’s good then that kryptonite isn’t actually Superman’s only weakness. The second most often cited weakness of Superman, by those in the know anyway, would be “magic”. Now, if a stage magician were to walk up to Superman and pop a flash paper thing in his face, that wouldn’t hurt him. No, it’s “real” magic that can hurt Superman. Essentially, if something can defy the laws of physics, nobody is going to deny that that could hurt Superman. That’s handy for characters like Mr. Mxyzptlk to befuddle our hero. So that’s another weakness, but still, he’s pretty overpowered, though, right?
Well, it turns out that if someone, or something, is strong enough, they can just beat the heck out of Superman. Really. That happens a lot for such an “overpowered” character. Look at the whole Doomsday thing. You know, that time Superman was beat so badly by some alien monster that he was declared dead. That was just some alien that happened to be strong enough to take on Superman. No magic or kryptonite involved. Other such monsters can and do exist in Superman’s world. You want Superman to feel threatened in a story? Throw some monster in there. Bam, he’s threatened.
But apart from that Superman is still overpowered, right? He can fly, he can shoot lasers from his eyes, he can see through walls, and more. What kind of villains are supposed to compete with that? Well, here is where I will remind you that Superman’s gallery of villains includes about a dozen people with the exact same set of powers that he has. The Phantom Zone is full of other Kryptonians who’d just so happen to love to kill the guy. Some, like General Zod, have Superman’s powers plus the tactical skills of a military leader. Some, like Faora, have Superman’s powers plus extensive training in martial arts. Some, like Nam-Ek, have Superman’s powers plus other mutations that actually make them more powerful. Some, like Jax-Ur, have Superman’s powers plus a scientific mind that could probably come up with clever ways to use those powers like Clark regularly does. They are at least Clark’s equal in powers and they outnumber him on top of that.
Furthermore! There’s all the other supervillains with powers. Bizarro has as many powers as Superman, but with bizarre twists. Parasite can drain Superman’s own powers at a touch, weakening the hero while buffing himself. The Cyborg Superman can whip up whatever technological nonsense you want to use that week. Toyman or Prankster can design any kind of wacky scenario in which Superman is threatened by some weird doomsday device. The list goes on.
As I’ve said before, I don’t think every Superman story should be about villains. I prefer to see him in stories that aren’t about who wins fights. But let’s suppose you want to tell such a story. And you don’t want it to be one where Lois or Jimmy or Ron or even Metropolis as a whole is in danger. You want to make it seem like Superman himself is threatened by a supervillain. But you don’t want the villain to have Kryptonite, or magic, or to be particularly strong, or have any interesting powers or to create an interesting scenario. In that case, I would suggest you just make Superman say “Man, it’s strange, but I’m feeling really weak right now.”
Yeah, that would be bad writing, but it sounds to me like you’re aiming for a bad story, y’know?