Several speculations/thoughts/questions:
First, did baby!Harry actually in fact survive the killing curse? ie, perhaps the curse successfully detached baby-Harry's-soul (presuming that something like "souls" exist in MoR... given the presence of Horcruxes, I'll tentatively assume yes), but the body was immediately made into a Horcrux... so Voldemort-soul-shard effectively inhabited that body. Essentially Rationalist!Harry is actually more like what Voldemort would have been like if raised in a loving and sci-fi and science loving family.
The Hat did say that if there was bits of the Dark Lord's mind there in addition to Harry, it would have noticed the extra "passenger"... But in this case there really is only one mind/soul/whatever. The catch is that mini-mort is all that's there.
This brings up the possibility of if this was an accident or deliberate. Perhaps Voldemort actually deliberately planned/faked his apparent "death"?
(Possible related, well, possibility: How do "we"/they actually know Voldemort even used the Killing Curse that night, as opposed to doing some other thing? ie, how is it known that he is the Boy Who Survived the Killing Curse in the first place?)
Further speculation: When Quirrellmort was lecturing in class about how he used to want to be a Dark Lord, but now finds that he really just wants to teach how to fight and such... perhaps that's a literal statement of fact? ie, does he even desire to "rise again as the Dark Lord Voldemort", or is this what he actually wants now?
Further further thoughts: Does Dumbledore know that Quirrell is really Voldemort under-the-hood? Not just knowing "there's something odd here", but actually really knowing that as fact?
perhaps the curse successfully detached baby-Harry's-soul [...], but the body was immediately made into a Horcrux... so Voldemort-soul-shard effectively inhabited that body. [...]
Further speculation: When Quirrellmort was lecturing in class about how he used to want to be a Dark Lord, but now finds that he really just wants to teach how to fight and such... perhaps that's a literal statement of fact?
This is awesome. Probably not where the story's actually headed, but it would create a cool Vader-Skywalker kind of relationship and explain what Voldemort...
Update: Please post new comments in the latest HPMOR discussion thread, now in the discussion section, since this thread and its first few successors have grown unwieldy (direct links: two, three, four, five, six, seven).
As many of you already know, Eliezer Yudkowsky is writing a Harry Potter fanfic, Harry Potter and the Methods of Rationality, starring a rationalist Harry Potter with ambitions to transform the world by bringing the rationalist/scientific method to magic. But of course a more powerful Potter requires a more challenging wizarding world, and ... well, you can see for yourself how that plays out.
This thread is for discussion of anything related to the story, including insights, confusions, questions, speculation, jokes, discussion of rationality issues raised in the story, attempts at fanfic spinoffs, comments about related fanfictions, and meta-discussion about the fact that Eliezer Yudkowsky is writing Harry Potter fan-fiction (presumably as a means of raising the sanity waterline).
I'm making this a top-level post to create a centralized location for that discussion, since I'm guessing people have things to say (I know I do) and there isn't a great place to put them. fanfiction.net has a different set of users (plus no threading or karma), the main discussion here has been in an old open thread which has petered out and is already near the unwieldy size that would call for a top-level post, and we've had discussions come up in a few other places. So let's have that discussion here.
Comments here will obviously be full of spoilers, and I don't think it makes sense to rot13 the whole thread, so consider this a spoiler warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.