Perhaps also germane is that I am not personally a believer in Less Wrong-style rationality, and so the intellectual content of the work was not relevant to me except in the detached way that philosophical or political or religious schools can be interesting to non-adherents (which is one reason I read as much as I did.) Whether the story accomplishes its actual goal, then, is something I can't judge, but I can say that, as a non-rationalist (irrationalist?) I didn't find it to be a good or engaging story.
But as I said in my previous comment, this is my own reaction, and I include it for informative reasons, not because I think others should necessarily share it!
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.
My personal experience with Less Wrong-style rationalism, to simplify the situation aggressively, is that it has a core of good, useful tools (Bayesian reasoning, strict positivism, utilitarianism) that I have no problem with. However, when pushed too far, those tools tend to break down—but the rationalist answer to that breakdown is all too often to embrace the model and discount the reality. This general refusal to regard their core tools with suspicion results in beliefs which are paradoxically irrational: when faced with e.g., utilitarianism condoning torture to prevent mild discomfort, the rationalist response is not, "Perhaps human experience does not map straightforwardly to integers—we should re-examine our tools," but rather, "As our mathematical tools are of course correct, we must believe in this conclusion." This belief in math-over-matter is a major part (though not the only factor) in my skepticism towards the kind of rationalism promoted by Less Wrong.
The strongest argument against rationalist utilitarianism seems to be that people don't like the cognitive dissonance it imposes on hypocrites.
http://lesswrong.com/lw/n3/circular_altruism/
And calling people hypocrites because things like involuntary organ donation gives them "cognitive dissonance" is absurd. Also regarding hypocrisy, note that Yudkowski works for an organization whose goal is to protect humanity from Skynet, while people in Africa are starving. (I'm not personally attacking him, he can work on whatever he likes, and I think governments of wealthy nations have both the resources and responsibility to alleviate starvation, and individual efforts are mostly pissing in the wind. But parent poster brought up sweatshops &c. so I went there.)
I'm unwilling to post spoilers, which makes this unfairly undiscussable, but the meaning of the original prophecy did not--could not--come down to rationalism and could not for reasons that were repeated a few times through the fic. I can't tell if this was intentional on Yudkowsky's part, and I don't really care, since it really changes nothing about everything else.
For the record, though, when I disparage utilitarianism, I promise it isn't just "Eliezer's".
No, they've said "this is a reductio ad absurdum, perhaps reality is a bit more complicated than that." You don't get to assert your assumption - that simplistic utilitarianism works as advertised - as evidence.
Consider, for instance, minmaxing as an alternative. (Like real-life AI work tends to.) What answer does that give?
The thing is... HPMOR isn't about the scientific method. It's about rationality. It's not a story about distilling a universal theory of magic or triumphing over death; it's a story about a kid who's had a rationalist education fumbling his way through a world that refuses to actually make sense.