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.