[SkyHejhogianMaestro]

It seems that the female gender is much more quickly labeled a Mary Sue...
Before reactions flair, let me say that I'm well aware of Gary Stus. Just note that- if you look at my butchered username- I happen from the Sonic/Dragon Ball Zverse before branching out. In these respective franchises, it took heavy debate just to convince a few people that several male characters were Gary Stus (despite in two cases actually being referred to as immortal, nearly perfect Ultimate Lifeforms) but when we had even barely competent female character (with strength or social class or relative proximity to the main characters), the terms "Mary Sue" flew left and right at staggering speeds.
Comparing 20 page debates on whether male characters are Stus with heavy and fierce criticism towards the accusers and defending the male characters only for CULTURAL MARXISM!!!1!!! to take its toll and, 5 years later, people begrudgingly admit that the male character is kinda, sorta like a Gary Stu but not in all aspects!!!... but this female character who can defend herself, oh dear god, kill this sue with fire!!!
So perhaps some fandoms simply are more liberal with their usage of the term, damn liberals, the Satanic Muslim feminist communist fascist anarchist anti-God SOBs. It's their fault that men can't be the all-powerful master race of complete competence and glory. Why can't they accept that women's place is in the kitchen making babies or cheering on their male companions- why should they even be in fiction?! Why does fiction have to have women at all? It's all a Zionist-Maoist-Lennonist-Bieberist plot to destroy the Church and the Family, I tell you.

In all seriousness, in studying the phenomenon there are certain instances where a character who is otherwise a Mary Sue/Gary Stu is "saved" by some sort of device. Think of Superman- he's the ultimate Gary Stu except he has a weakness- Kryptonite. This allows there to be diverse plots. If you introduce Kryptonite, you cripple the second most powerful fictional character in history. Sure, it's a plot device now, but it does prevent him from become an outright Gary Stu. Also, he is wish fulfillment. When the purpose is wish-fulfillment, sometimes I do have a soft spot. When it's so poorly written, then there's a problem ala Crisis-age Superman/Superman Prime where he was literally God.
That's just a typical non-anime example but I hope it gets the idea across. One of the better reasons why I do see some women being labeled Mary Sues legitimately is because some authors decide to create competent females but decide that omnicompetence with an added dosage of sexual satisfaction is "competence."

But that's not it either.

Character matters the most of all- particularly, how things respond to the character. If this perfect character is also so awesome that the Laws of Physics unconvincingly warp just to allow them to do their awesomeness unabated then you're probably dealing with a Sue.
If this character is so beautiful that light itself shines brighter around it and somehow calls to notice their curves/definitions and turns the most flat, apathetic grump into a nearly dogmatic follower of the character (either by sight of their face or by the perfect sound of their voice) or if they need to destroy a black hole and come up with an idea on the fly that doesn't make sense and it somehow DOES destroy the black hole and they're forevermore worshipped as smarter than Einstein x5000, then...