I know that some people have a hard time with Kryptonite because they think it's silly for the world's most powerful man to be weak to a "glowing rock." I like to think of it as Superman being continually haunted by the death of his native planet. Krypton's destruction is what made him Superman by forcing him to Earth where he gained his miraculous powers. It's also a great tragedy since he'll never get to know his own people and since he will always be a bit of an outsider on Earth. To me, Kryptonite has always been the physical representation of this. The home that had to die so he could be great haunts him and brings him nothing but weakness. Besides, it's a classic piece of his mythology. Can you actually imagine reading Superman comics without any Kryptonite?