It wasn't apparent in my own comment, but I don't put much stock in the "intellectual content of the work" myself. I dislike LessWrong and self-described rationalists, including Yudkowsky as far as I know him. I agree with su3su2u1 that, insofar as Yudkowsky intended HPMOR as a pedagogical vehicle, it was not really well done.
That said, it is rare that a work of fanfiction manages to be a legitimate deviation and self-contained work that both comments and reflects upon its originator usefully. Generally speaking, I prefer to give all fiction the benefit of the doubt: whatever its failures, it is hard to ignore that it was successfully written and as someone who has tried my hand at it, I know firsthand the challenge overcome. There's a "Man in the Arena" quote insertion that belongs here. I did find it to be a good and engaging story, though, if painfully in need of an editor, which is not a unique remark in the land of fanfiction.
If you want to really have fun, compare HPMOR with the Left Behind series, which qualifies as fanfiction as much as anything. There are probably some fascinating parallels to be found with their relationship to their original works and author intentions and the like. You can find a much higher quality counterpart to su3su2u1 in Fred Clark's Slacktivist blog, which dissects it on a page-by-hilarious-page basis.