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I'm not a fan of Mary Sue (and Gary Sue) for two reasons. The first: lack of character development. Writers of Mary Sues are so desperate to live out their personal fantasies that they typically forget character development. Because the Mary Sue character is so perfect (and predictable) there is no growth or mystery. Mary Sue is nothing more than a flat character. The writer also fails to answer the important question: why should we care about this character? Writers of Mary Sue assume that if their character is an all-mighty-powerful being it'll make up for a lack of unique personality/background, as if we'll LIKE that character and think they're 'bad-ass' and 'awesome'.
Uhhhh. NO.
Introducing flaws or traits that readers can relate to is the best way to open up to that character. Unfortuantely, Mary Sue DOESN'T have flaws or traits we can relate to. And if she does have a weakness, it's usually some superficial/ridiculous one.
So this is the first reason why I hate Mary Sue: she's flat, predictable, ridiculously unbelievable, unrelatable, and BORING.
Another reason I don't like Mary Sue: it prompts the star of the fanfic (the one we love/recognise and the reason why we're reading the fanfic in the first place lol) to do/act/say something out of character. Because the fanfic REVOLVES AROUND MARY SUE, characters we love act, well,... stupid.
Case in point: Devil May Cry's Vergil. This son-of-a-bitch is a ruthless, indifferent man who would do anything for power. I'd find it VERY HARD to believe that he would suddenly forget about world domination so that he could live out his life carefree with a giddy girl who happens to be 1/9th angel, 1/8ths neko, 2/3rds demon, and 4/5ths sage.
Riiiiiiight.
So there are my two reasons for Mary Sue. She messes with the characters I love.