I think Eliezer probably meant us to know that Quirrell was H&C the very first time he appeared.
I disagree with this at least as strongly as you believe it. I'm pretty sure he meant Hat and Cloak to be a giant question mark. Hence the elaborate descriptions of the broad hat, the dark mist, and the gender-concealing cloak, all drawing your attention to the mystery of his identity. There have been hints, but they don't all point in the same direction the way they do for Quirrell and Voldemort. Some are red herrings. I conclude that we're not meant to be certain of who he is. We're meant to wonder and doubt.
(The HPMOR discussion thread after this one is here.)
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. There haven't been any chapters recently, but it looks like there are a bunch in the pipeline and the old thread is nearing 700 comments. The latest chapter as of 7th March 2012 is Ch. 77.
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.
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.
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: