Superman does have weaknesses. Besides magic and kryptonite, his main weakness is that he always does what's right and cares about all life. His foil is Luthor, who has no moral compass. As far as superpowered heros go, in effect, Superman isn't all that different than Thor or the Hulk. Once you get to having a being of that power, you need to get creative with the writing.
Writing a great Superman story isn't all that hard IMO. The best ones have a combination of slugging it out with an equally powerful foe and mental games with a morally corrupt foe.
There are lots of good Superman stories out there.
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