Well, the Mary Sue Litmus Test may not be killing our characters directly (that's the job of the villains, right?), what it is doing in encouraging writers to create perfectly average, mildly attractive, IQ of 102 characters. While these characters usually aren't Sues or Stus, they're boring.
You can have an extraordinary character. You just have to be careful not to overdo it. See here.
Let's say your heroine can somehow control fire. Fine. If she can speak three languages, okay. It's when you start piling on things like incredible beauty, skill with every musical instrument, and instant perfection at everything she does, and have the story hand her everything on a silver platter with no work or sacrifice, that the character starts turning into a Sue.
Think of the Mary Sue traits like garlic when you're making pasta sauce. A little garlic can make that sauce taste a lot better, but add too much and you won't want to have anything to do with it.
Even a lot of things that people consider Mary Sue traits really aren't. A lot of the "traits" on Mary Sue tests either; could apply to any character or real-life person, have nothing to do with the story itself, or are taken completely out of context and ignore any justification the story provides. Here are a few examples from popular tests and my comments.
"Does the character have a name you really, really like?" - In most cases, yes. I control the names of the characters. Why would I give them names that I didn't like?
"Does the character have a nickname or pseudonym?" - Last I checked, most everyone has a nickname. My full name is Maxwell, but lots of people call me "Max", "Max-o", or even, "Maximus". Oh no, I'm a Gary Stu!
"Does the character play a musical instrument well?" - Oh no, my dad's a Gary Stu too! This would only apply if the character learned how in a very short amount of time.
"Does the character have a physical handicap that does not hinder her/him significantly?" - I'm near-sighted. But I wear glasses, and even with them off I can still see well enough to not get myself killed. And to think that adds 6 Stu points to my record.
"Is your character top of her/his class?" - But... every class has a top. Are all of those people Sues?
"Is the character bullied for her/his sexual orientation, skin color, intelligence, poverty/wealth, looks, clothes, background, etc." - That's actually fairly common, and shouldn't be a Sue trait unless the character uses it as a cheap excuse to angst.
"Does the character use Japanese words in conversation, although she/he does not live in Japan?" - "Shut it you baka! This is so kawaii, desu!" While people like that may have problems, they aren't Sues. Also, por qué en la tierra is it only Japanese words?
"Is the character fluent in more than two languages?" - What if the character is a translator, or an ambassador, or a trader who travels around a lot? Also, there are a lot of immigrant families out there whose kids speak both the language of the new country and that of the old for communicating with older relatives. Are they all Sues?
"If not a cross-breed, then at least cross-cultural?" What? Do these people have any idea how many people out there are cross-cultural? I'm Russian, Romanian, German, Norwegian, and French Canadian, with a few other things probably mixed in. Am I a Stu?
"Is the character rich or well-to-do, although she/he doesn't work?" - One word: Inheritance.
"Is the character astonishingly good at something that is not her/his profession?" - There are a lot of people who are good at things that aren't their profession. I'm deadly accurate with a Nerf gun, but my job certainly doesn't have anything to do with guns. (For those who are curious, I work at a newspaper)
"Does the character talk about anime frequently or have lots of anime clothes, collectibles, etc.?" - I don't see how this is a Sue trait. The person has a hobby, albeit a slightly obsessive one. Who cares? And why is it only anime? I think that the person who wrote that particular test has some odd hatred of Japan.
Get this in your heads, people. Subjectivity. Context. Justification. Logical sense. These seem to be foreign terms to the people who make the tests and those who swear by them. Don't make a character boring (or worse, all flaws and no good qualities) so that you score a few points less on some lame test.
Having magical powers does not immediately equal Sue unless the character is the only one with said powers or is freakishly strong for someone of his or her age or experience level.
Having a certain color of hair does not equal Sue, unless the character has a natural hair color that is physically impossible for that character's species.
Being able to fight with a sword or other weapon does not make a Sue unless the character rose way too high, way too fast (such as a character being able to defeat all of his vastly more experienced teachers after just a few weeks or months of training).
Being beautiful or handsome does not equal Sue unless it is taken to an extreme level. Examples would be a character so attractive that they cause traffic accidents, one so attractive that everyone either wants to kill them or date them, or one so attractive that they can make anyone fall in love, even someone who is asexual or sworn to never fall in love.
Being highly skilled at something does not equal Sue unless the character reached that level in a very short amount of time or it is very unlikely that the character would ever have had the opportunity to learn it. For example, a rich girl who's an expert hacker would make sense, as she probably has a lot of spare time and money and probably not too much parental supervision. A person living in a poor neighborhood who works two jobs just to make ends meet and doesn't have a computer, not so much.
Heck, even Tragic Pasts are subjective. They're generally only Mary Sue traits if they're only used as cheap excuses for the character to angst or let the character get away with crimes or other bad deeds. ("Oh, it's okay that you accidentally pushed the general into the volcano. It was clearly caused by the trauma of your Tragic Past.")
I would recommend reading this analysis of a Mary Sue Litmus Test. (Link updated September 6th, 2010)
You may be wondering what I consider to actually be legitimate indicators of Mary Sues. Well, here you have it:
1. Characters who look exactly like the author or an idealized version of the author (ex. 6 inches taller and with an 8-pack).
2. Characters who have no physical flaws (except for sexy X-shaped scars on their face) or personality flaws.
3. Characters who are instantly perfect at everything they do and never make major mistakes.
4. Characters who never have to struggle or sacrifice to get what they want.
5. Characters who have amazing powers and abilities, far beyond what is considered normal for the story's universe, and that have few or no downsides or limitations.
6. Characters who are instantly loved by everyone else, even the most cynical and jaded characters. Their plans are always favored over those of people with far more experience and they are always forgiven for mistakes.
Numbers 2-6 are the ones that I think are instant indicators of Mary Sue status. However, there are only five of them. And I daresay that most writers are better than that.
So don't be afraid to create a character with the logical prowess of Sherlock Holmes, James Bond's fighting skill, or Christine Daae's singing voice. Don't be afraid that people will call you a Suethor the second your character actually does a good job at something or gets off his butt and does something cool.
http://maxhelmberger.com/thoughtsmarysuefear.html
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