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Batman
If a human i.e. Lex Luther can have Superman on his knees with a little Kryptonite then Batman with his super cool gadgets, as well as intelligence, could easily destroy Superman.

Very true. Like you said, Superman is totally disabled by a little kryptonite. But Batman doesn't really have a kryptonite, therefore, making Batman stronger and better.

Batman hands down. One is an alien one is a human and Batman still holds his own :)