There's a lot of stuff in the fic that's explained only indirectly, leaving the reader to infer the truth - the Pioneer Plaque horcrux; Malfoy's belief that Harry is Voldemort; that Dumbledore is partially responsible for the potion that cleared up Petunia's appearance; the solution to Rita Skeeter's mistaken evidence (though that was made explicit recently); Skeeter's death; the self-serving nature of Quirrell's "strengthening" of Harry (learning to lose, inability to testify under veritaserum, rescuing a former minion, etc); the list goes on...
The new thread, discussion 13, is here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With three chapters recently the previous thread has very quickly reached 1000 comments. The latest chapter as of 25th March 2012 is Ch 80.
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, eleven.
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: