The problem has nothing to do with mages, but rather with a disparity in power level between player characters; the exact same argument could be extended to any class. Not every knight is as skilled as Sir Lancelot, not every barbarian is as strong as Conan, and not every mage is as powerful as Merlin. Place any heroic character into a game where the other characters are non-heroic and you're going to run into balance issues - even that 'farmer' PC is going to be seriously overpowered in a mud where the rest of the PCs are farmyard animals.
But that doesn't mean you need to make knights, barbarians, mages or farmers 'uncommon', only that you need to consider how balanced they are against other character concepts within the gameworld you're designing. Place Merlin in a game where the rest of the PCs are gods, and he's going to suck.
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