To an extent, I agree; however, two quasi-defenses:
1: It does actually get less Mary Sue-ish as time goes on; a large part of the purpose of the starting chapters is to establish Harry as a rationalist badass, and once that's been established that element of his character becomes less prominent- see, eg chapters 10, 18, 30-31, the whole Azkaban story arc, and probably a few more.
2: A major purpose of the story is to be awesome/to show a rationalist being awesome. (Also, it's explicitly influenced by another story often accused of Mary Sue-ish ness, Shinji and WH40K.) If it didn't skirt close enough to the edge of Mary Suedom to be perceived as an outright Mary Sue by some, it wouldn't achieve its goals.
I've been hearing about this fic for a long time, and I've been somewhat suspicious of it. I knew that Eliezer is a pretty good writer, but that his attempts to graft Bayes onto his characters are invariably rather inorganic. On top of that, OOC is irritating to me even when I expect it.
Nothing, however, prepared me for this. I just got done reading chapter 6. Up to this point, Harry's greatest sin was dumping a Less Wrong post onto poor Minerva every ten minutes. And she understood everything, including pop culture references (when in the books, most wizards don't comprehend rubber ducks).
Now, in this chapter, Harry thought he heard a strange note in the prof's voice, decided in a split second that she's trying to destroy his parents, and informed her of this suspicion in the form of a hissy fit. Then he started blackmailing her, and finished by implying that she's a nearsighted idiot, but it's alright, most people are. And he started calling her McGonnagal, then switched to Minerva, and is now planning on Minny for the future. I expected her to snap at some point and beat him to a pulp with the first heavy object that presents itself.
I read the reviews pertaining to that chapter. They all proclaimed it to be a masterpiece, the standard by which all other fiction should be measured. To me, it was what people call "epic fail". I cannot find any other way to describe my reaction. Calling it terrible just doesn't have that drop of vitriol that I think is necessary.
But this is Eliezer Yudkowsky. I KNOW he can write. I KNOW that he can detect and neutralize a Black Hole Sue. And yet...
Does he?