One problem with it is that it at times it feels like very much like EY's mouthpiece.

Fair warning, I talk about this point a lot. There's a subreddit and I think it's the only non-sports reddit I check daily. I'm committed.

I think, first of all, that it's valid to say the story is his mouthpiece, but not to use that as a criticism. His stated purpose in writing the story (and the one that allows him to use work time to write it) is spreading his ideas far and wide on the internet. If the medium didn't allow the story to be his platform, the story wouldn't exist. The man's a genius; HPMoR is his first full-length writing of any sort and it's already the most popular piece of fanfiction ever written in terms of reviews and favorites and word of mouth. So it worked.

And thousands of people don't see that as detracting from the story, which is my second point. Even if you don't dig the extended sections where, say, Harry is attempting to teach Draco that the antagonists' concept of "blood superiority" is irrational by using entry-level genetics (and it's working, because in HPMoR all the primary characters are actually intelligent, but also not working because Draco is the equivalent of an 1830s plantation owner's son) -- even if you aren't into those bits, the common complaint from everyone who is is that in the last 30 chapters we've gotten nothing but plot. Yudkowsky's storyline eventually forced him to leave the mouthpiece at home to a large extent. And everyone's still reading. Because it's a damn good story even if you disagree with every single tenet of LessWrong rationalism, or don't want to hear the scientific method mentioned in the context of discovering why and how magic works in JK Rowling's universe. (But really, who doesn't? That stuff is far more interesting than the original series.)

I'll cut myself off there because you almost certainly don't care about this as much as I do.