Way too many.
But to add something, if you want to look for the worst of them, just look for the ones in drama heavy shows. While they may not have the same trophes that distinguish other anime genres, the drama genre is infested with their own kind of toxic repetitive material. That somehow this escapes the scrutiny of critics is nothing short of baffling.
Oh and yeah, the Mary Sue is one among them. If I had to describe them, they are even worse than from other lightheaded settings since the dramatic, more realistic tone of these shows makes them even more unrealistic and intolerable. As a general rule, the universe will bend to make them cool/correct. It doesn't matter how reckless/unorthodox they are, they'll always be right. And if something goes wrong it's outside of their control (and the story will make that clear) and most likely used to steal some sympathy from the audience. (For an otherwise unrelatable character)
I love her theme, but she's just a bit too much if you ask me