I think that the story leaves a lot of uncertainty in its depictions of other characters' disposition towards Harry and each other. We still don't know what level Dumbledore's playing on. Did he notice Harry in the prison cell (he could, since he might have mastered the deadly hallows)? Did he connect the hole in the wall or transfigured rocket fuel with Harry's magic style? Could he stop rocket-powered broomstick in time? Is he Santa Claus? Did he mislead McGonagall to try the flawed test? Did he prompt Snape to confront Quirrell at Mary's Place? What does he know and suspect about Quirrell?
McGonagall seems to be irrationally optimistic about everything and hopeful about Harry. Snape underestimates Harry, or at least doesn' t interfere with him all that much. Mad-Eye doesn't know Harry personally, or else he would probably instantly unravel all of his plots and half of Quirrell's and Dumbledore's for good measure.
Update: Discussion has moved on to a new thread.
After 61 chapters of Harry Potter and the Methods of Rationality and 5 discussion threads with over 500 comments each, HPMOR discussion has graduated from the main page and moved into the Less Wrong discussion section (which seems like a more appropriate location). You can post all of your insights, speculation, and, well, discussion about Eliezer Yudkowsky's Harry Potter fanfic here.
Previous threads are available under the harry_potter tag on the main page (or: one, two, three, four, five); this and future threads will be found under the discussion section tag (since there is a separate tag system for the discussion section). See also the author page for (almost) all things HPMOR, and AdeleneDawner's Author's Notes archive for one thing that the author page is missing.
As a reminder, it's useful to indicate at the start of your comment which chapter you are commenting on. Time passes but your comment stays the same.
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: