"She is without a single minus?" Only as someone said before, she's stubborn, and this directly results in her getting captured at one point in the story, and the story arc involves her learning to be more social and learning to trust others to help her in the final battle.

It's fine if you don't like her as a character and it's fine if you were bored by her character arc, but parts of your analysis of her are objectively wrong. "Mary Sue" means something specific and she's not one. She has very clear faults, these cause her direct consequences in the story, these elements aren't subjective interpretation, they're factual description of the game's story events unfolding.