Though I've always considered Frodo a Mary Sue. Basically, I never saw a reason why the author seemed to think he was so awesome except that I kept being told how awesome he was (unlike, say, Sam, who was obviously acting awesomely because he, say, cooked dinner ;-))
The reason Mary Sue is a gendered term was because it was invented in a predominantly female environment. That is, it was women reading writings by women about female characters, so it referred to female characters. Wesley Crusher and the reaction to him I think demonstrates that the concept isn't inherently gendered, even in that fandom. Fundamentally, people don't like characters that the author likes more than we do.
It is absolutely misogynistic to apply different standards to male protagonists than female protagonists, but that doesn't mean we have to like glorified protagonists of any gender, especially when accompanied by tell over show writing. I tend to think we overrate books about male protagonists on general principle (this being The Great American Novel problem). It's part of why I'm a big fan of authors that write about ensembles of variable characters instead.