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Illyria
Oh I agree that Mary Sue does get used a lot and often inappropriately. But to me, there's a few universal traits regardless if they're the black hole sue, the purity sue, the tzun sue, etc.
Usually, if the character is written in a way that is meant to portray them in a favorable light, right down to tossing in flaws that can only enhance their likability, that alone won't make it easy to point out. But if they do something that ought to have negative consequences and is out of character for others to ignore or even handwave it, then that calls it into question. For example, if a character who is sweet, kind and has the power to invade other people's mind to take control and does this to her friends frequently to prank them, who would ever be comfortable around her, let alone forgive her without an earful of rage at her violating one of the most basic tenets of personal boundaries?
Another trait is when a character starts to acquire talents that are unrealistically outside their current experience and control, even within fictional settings. Becoming the head of a spy organization when they start off in a career that has no transferable qualifications raises eyebrows and should be examined.
This all can be turned on its head of course and there will be characters who can have all those traits but be written where it's believable.
I guess, I want to say that when I use the Mary Sue label, it's not done without a lot of thought. I can't stand Bianca. I would not miss her if she wasn't there in the next Dragon Age game. But she is not a Mary Sue. Her arrogance makes sense. She IS talented in her smith work and her skills remain firmly with her background. She was raised in the Carta so she would know how to fight, how to be cautious and discreet. But, she does mess up. And Varric has a very understandable reaction though he still loves her because of their history. Despite her groundbreaking revelation, it does nothing to distract from her mess up. She's interesting in that I suspect she's used to being praised for her skill and given a lot of allowances by her family because she gives them prestige. So the one time she can't get everyone to drop their frustrations with her despite her efforts to make up for it, she lashes out in a way that's disguised as altruistic concern.
In short, I think she's well written, albeit in a frustrating manner.
One final thought: I think what makes the Mary Sue label so reviled to the point that fans of characters will fight tooth and nail to prove it wrong is because the story and the characters around the accused "Mary Sue" suffer in its midst. Logic takes a nose dive like why would a ruler give this character that much power over the kingdom just because there's something special about them? Or why haven't we heard more about others that interact with this character? What's their background and why do they like this person?