A few points
Hat and Cloak almost slipped and said time travel.
Mary sue time travel is a common device in fan fiction.
The author has stated MoR includes elements that are necessary to ensure artistic completeness as a work of fan fiction.
Mary sue time travel was derisively referred to in the same conversation in which the idea of Sirius Black conspiracy theories were debunked.
There is a person in Azkaban who endlessly repeats "I'm not serious" (Sirius).
It is not possible to travel more than 6 hours back in time with a time turner.
Prophecies transmit information further back in time than 6 hours.
Atlantis was erased from time.
The Weasley twins remark that the Marauder's Map is showing errors.
The Sorting Hat still works.
From the above, I suspect that Mr. Hat and Cloak is a time traveler who has an earlier version running around in the present.
(The HPMOR discussion thread after this one is here.)
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. There haven't been any chapters recently, but it looks like there are a bunch in the pipeline and the old thread is nearing 700 comments. The latest chapter as of 7th March 2012 is Ch. 77.
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.
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.
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: