Superman has 3 weaknesses. Kryptonite, Lois Lane, and an aversion to killing.
It's only really one thing.
Unless the villians have kryptonite, they cannot physically harm him.
They can abduct and get Lois, but as we seen in one of the movies, superman can make time go in reverse and save people.
He cannot see through lead...that might be a weakness but it cannot harm him.
The aversion to killing is not really a weakness. He can pretty much catch any bad guy he wants to without killng them....as long as they don't weaken him with Kryptonite.
That has always been the problem with Superman.
He has no true enemies that are equal or who can truly threaten him time and time again without a piece of Krypton which is extremely rare.