For me at least, even knowing the that Q=V, and seeing the clues, they don't intrinsically point to that. Most of them can be explained simply by the idea that Quirrell is subtle, evil, and likes corrupting people.
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.
I hadn't read the original series either, and so at first I had no idea that Q=V except from the Author's Notes; however, I suspect that by this point in the story I would have begun entertaining it seriously as a hypothesis. (And of course as long as the story is still being written, there's always some chance Eliezer could change his mind.)
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 substa...
[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.