I'd say lower probability, but Snape is the obvious villain right now based on what we know about him destroying the notes
Wait, how is this relevant? Destroying the notes is just about cleaning up his SPHEW-related tracks (due to his apparent embarrassment at being a soft touch w/r/t bullying) now that Hermione and her notes are under great scrutiny as possibly being related to her framing.
And in fact, I'd say the notes are evidence against. If Snape had been plotting this all along, one might expect the notes to have been destroyed before the incident is uncovered, say after Hermione left for the duel, since Snape would not be able to guarantee he'd be assigned to look for the notes, that he would be alone or unobserved in every way, etc. If you predict an investigation will find dangerous papers you no longer need, you don't wait until the investigation starts!
I don't see Snape's motives the same way. Here's why I think he's the obvious villain (if my above 'twist' is wrong :/):
We know he was behind the plot with SPHEW as the puppet master, and that it centered around Hermione. As a result of his involvement, the bullying situation escalated until Dumbledore had to end it. If not for Malfoy's involvement at the cafeteria, Hermione would have ended her anti-bullying crusade disgraced, embarrassed, and powerless. The fight with the 7th year had the potential to end things in this way with Hermione as well, but...
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
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.
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: