Agan, I think this whole thread has been about fan-fiction Mary Sues- and a lot of the reason people complain about them is their habit of taking over from the actual characters, in a general "anything you can do, I can do better" way. They're more beautiful! More talented! They have bigger and better angst! They're the ones who really save the world!
When you start applying the same criteria to characters in original fiction... then, yes, it becomes problematic. Not that "canon Sues" don't exist, because of course they do, but the definition is often stretched so far that it becomes meaningless. Not only that, but some people definitely do seem to use a simple equation of "female protagonist = Mary Sue".
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"Even Nerwen wasn't evil in the beginning." –Elmo.
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