The underlying theory- that Houses correspond to aptitudes / personalities rather than goals- is mistaken. That's something Harry is mistaken about it too, so don't feel too bad about that. (That's one of the reasons he's so bad at modeling others.)
Your other observations appear correct, and the outcomes you list are all plausible (though obviously not exhaustive). None of them strike me as particularly probable (except for the OR statement which encompasses most outcomes- the other option is that Dumbledore wants Harry's rage, just like Quirrel might, and so is deliberately not saving Hermione). Quirrel is a primary suspect behind this plot against Hermione, and gets more out of the Harry who has declared war on Wizarding Britain than the Harry who is grateful that Hermione was saved. McGonagall does not have the hero's disease that everything is her fault, and so is unlikely to see this event as under her control, and is thus unlikely to intervene.
Similarly, Lucius is probably Snape's closest friend at this point, given Snape's new understanding of Dumbledore's motives and lowered connection to Harry. Snape might have a crush on Hermione, but I don't think we have evidence to that effect and he would have to be totally mad in love to go against the Wizengamot.
Well, if Harry fell for it, then I suppose I can't be too bad... :P. But isn't that what Harry "hears" when he thinks in the personalities of Gryffindor, Hufflepuff, and Slytherin? (with Gryffindor and Hufflepuff usually tag-teaming?) If not, what does it mean? I'm guessing that it is his imagination (not, for example, Voldemort's Horcrux talking to him), but why else would E.Y. insert it into this story?
I agree that Quirrell benefits the most from Harry becoming so angry that he loses control in order to protect Hermione and is therefore probabl...
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author's Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven, eight, nine, ten.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: