> What is there in the story that indicates this judgment is wrong?
The ending? https://hpmor.com/chapter/122
> "Ah..." Harry said. This was very hard to say. "Actually, the rest of the world doesn't know this part, not even the Headmistress. But in point of fact you were one hundred and twelve percent correct about [spoiler], and I'll remember for future reference that although 'Dark' and 'evil' may not technically be the same thing, there's a great big statistical correlation."
> "Oh," said Hermione, and fell silent again.
> "You're not saying that you told me so?" said Harry. His mental model of Hermione was yelling: I TOLD YOU SO! DIDN'T I TELL YOU SO, MR. POTTER? DIDN'T I TELL YOU? [spoiler], I SAID, BUT YOU DIDN'T LISTEN TO ME!
It feels like most people who criticize the story didn't actually read it, and just start with the premise that Yudkowsky sucks at writing, then conclude that obviously Harry Potter must be Mary Sue, and that whatever Harry says is what Yudkowsky wants you to believe.
If you actually read the story, you will find out that many things that Harry said and believed turned out to be wrong. That ending was written by Yudkowsky, too. The characters that disagreed with Harry since the beginning, such as Hermione and Dumbledore, were written by Yudkowsky, too. Perhaps there is a little more depth in the story than if you assume that it must be a Mary Sue story.