A character's power is inversely proportional to their happiness.
Pete: What is superman's greatest weakness?
Pete: No...Lois Lane.You've got a powerful individual, at risk of becoming a Mary Sue, too high on the Super Weight scale, won the Superpower Lottery, or perhaps an Author Avatar. They possesses more power than they by all rights should. And you want them them as regular character, most commonly the protagonist. How do you balance them out? They can't overpower every opponent they face; they need a strong flaw. You could have compensation required for their abilities. Or maybe their powers have a weakness. Perhaps instead of making the character weaker, you make everyone else more powerful. Yet each solution has problems. Weaknesses can come up too often. There's only so much you can do to scale up other characters, leaving the risk of characters being left behind. Compensations tend to be set in stone, offering very little in the way of flexibility. How about taking a fourth option? Enter Superpower Suffering: "If they're so hard to attack physically, then maybe we should attack mentally?" This is not a Mind Rape. This is when a villain, instead of destroying their enemy directly with physical harm, destroys them emotionally, be it intentionally or unintentionally, making them miserable. A brilliant tactician can suffer a great failure, or have something they genuinely could not have stopped but feel like they should have been able to. A powerful warrior can have one of their loved ones be killed while the warrior is elsewhere, possibly fighting another evil. The more powerful the character is, the more this seems to happen. Take a look, for instance, at Lelouch's life in Code Geass: he catches no breaks and is constantly miserable. But he's a Magnificent Bastard with an overpowered ability, who has friends in all the right places. This is when the "strong flaw" of a character is constant misery. The more (over)powerful a character is, the more they have to suffer in order for the audience to believe they're still (relatively) human(oid). (Note: Needs a Better Title.)
-- Warehouse 13