If characters like Superman and The flash are really that powerful how do writers create situations where the villains are a challenge to defeat without everyone having to use kryptonite or whatever The flash is weak to?
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By making the villains equally powerful.
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By making the villains just as powerful if not more so, or making the challenge one that requires more than sheer power to solve. Kinda like Lex Luthor's schemes. He's just a human guy, but he manages to pose a serious threat to Superman by making plans that Superman can't just muscle his way through. Also, he's a powerful corporate executive with his own dream team of lawyers, when he isn't the President of the United States, so Superman can't just toss him in jail and leave him there.
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By making them as powerful as the plot allows.