Before we get off the subject of Mary Sues, I'd like to mention Possession Sues. These happen when a fic writer turns a canon character into a Sue. It's insulting to the character and the canon work. It can get especially bad if said canon character is a customizable character from a game, such as Commander Shepard, particularly when writers try to sidestep the issue by saying that since these characters differ between players, anything goes.
Which comes to a fic that had this down to a T. In this fic, FemShep manages to get the best possible solution concerning the Reapers by a sequence so convoluted I couldn't understand it (it involved jumping between the choices and hacking code and bunch of stuff that left me confused), she becomes the liaison to the Reapers (not controlling them), educates Harbinger about organics, her body changes to take on turian traits (this is a Shakarian fic, btw), gains some type of (I'm assuming) high position with turian government, and has a bunch of turians and Harbinger wanting to screw her because she's just so awesome and badass even though they know she's with Garrus. Come on, that itself is one of the most traditional traits of a Mary Sue! But the worst part? The writer has Shepard herself admit that she's a Sue! And then defends themselves (the writer) by using Garrus as a mouthpiece to point out that hey, Shepard in canon is practically a Mary Sue already, so it's all good (so what if she only succeeded due to the help she had, it was still because of her leadership anything got done; this was actually one of his arguments)!
Look, Shepard is a video game character, and as such, will almost always come out on top simply because if they don't, the player can't advance. Of course they'll appear to be an unstoppable badass devil/saint. But even canon has its limits. Renegades can have actions come back and bite them in the ass, paragons might be forced to concede to resolutions they don't want, and mixes can fail spot checks that result in undesired consequences. This fic Shep seems way too . . . I don't even know how to put it. If the things I mentioned don't seem too bad, it's much more obvious in the fic itself.
And on a final, major note, acknowledging that your character is a Mary Sue does not suddenly stop the Mary Sue from being an annoying Mary Sue. It doesn't make it anymore acceptable just because you've pointed it out.