The Law of Conservation of Detail (TV Tropes warning) implies that an important character who is subtle and evil (or even just subtle) has a substantial probability of being the villain.
But there are a lot of subtle characters in HPMOR; Quirrell might be the most subtle and the most apparently evil, but he's not the only one. That would imply that Harry, Dumbledore, and Lucius also have substantial probabilities of being the villain.
Edit: Then again... maybe that's correct.
On the other hand, I think we've been told to expect most characters to be substantially smarter than their canon equivalents, and maybe this kind of subtle schemingness just comes automatically when you have a bunch of smart wizards who don't trust each other and have potentially conflicting goals that they all take seriously as things-to-protect.
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
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.