One important thing, for those who find the main character insufferable at times: this is not a simple mary sue story.
When you notice Harry doing something dumb, oblivious, overconfident, condescending, etc. do not assume that this is the author's personality leaking through. It may be the intended reading.
I only read a little of it, but every time a character did something dumb, oblivious, overconfident, condescending, I braced myself for a thought missile.
In fact, Harry's personality is a Clue, or rather Bayesian evidence to use when predicting future events in the story, or deducing the true nature of the mysterious events that started the story.
Given that the early parts of the story are written in such a way that the narrative treats Harry's behavior as completely right and justified, it seems far more likely to be a retcon done years after the fact than some secret master plan Yudkowsky had in mind from the beginning.
The ending was explicitly foreshadowed in Ch. 1, including advance quotes. And, like, all the other early chapters. Nobody familiar with HPMOR could possibly take seriously the notion that this was a retcon.
No, but it's pretty close to one. Guess who bit his maths teacher at age seven when said teacher didn't know what a logarithm was?
Also, read this: http://lesswrong.com/lw/k9r/cognitive_biases_due_to_a_narcis... It's a perfectly normal literary analysis of HPJEV as a narcissist and/or raised by narcissists. It's not Ph.D-quality rigour, but it does back its claims. Note the amazing special pleading in the comments - fans outraged someone would dare analyse their favourite thing in less than glowing terms.
They seriously think they can get this thing a Hugo, somehow evading all artistic critique along the way.