If we ignore that it's a rewriting of JKR's 7 novel series, which gives it a certain amount of coherency, Yudkowsky violates almost every writing guideline in a bad way. In fact, I could probably write an infinitely long coherent essay describing the ways HPMOR violates a reader's mind. It would be easy given almost 700K source material.
But to point at some gaping holes, the plot has no pacing, and the entire story is a badly written self insert where the mc goes around and "fixes" JKR's plot-holes by writing themself into a corner.
The solution to this, is, of course, to write another 20K words of expecto patronum, dispel the plothole with more rationalist bullshit.
Your average fanfic is probably better written.