It is a damn high bar and I think you mentioned the big players. Dumbledore -> McGonagall is easy. Then it is Snape vs Flittwick for No.3. It wouldn't seem unreasonable to place Snape higher than the gnome illusionist given that Snape is the one with dark secrets that no doubt include all sorts of badass juice. The problem with the '3' figure in MoR is that Quirrel comes in as a wild card and you would be reckless place him anywhere below second. And as you say, Snape > McGonagall doesn't seem right!
This. I feel like Quirrell would never fight completely fairly against anyone and so he basically can only lose against the unbeatable power of the elder wand. In a fair fight Snape and McGonagall together might be able to take Quirrell but doesn't fight fair.
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
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. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, and AdeleneDawner has kept an archive of Author's Notes.
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: