Falsely Advertised Accuracy: The author has a tendency to grossly simplify points that are actually under debate, and to simply state his preferred interpretation as unquestioned scientific truth. The most blatant is that his specific interpretation of Bayes' Theorum is not only treated as the only one, but as the same thing as the scientific method.
Schedule Slip: Around Christmas 2011, nearly four months after Chapter 77 was published, Chapter 78 was finally done, but to spare the readers the nerve-wracking wait between its cliffhanger and Chapter 79, the author decided to finish Chapter 79 first. When that one was finished three days later he then decided to finish the whole arc first because his speed had improved so much.
But three weeks later, he was already finishing chapter 81 and explaining that he was still making backwards edits to all the unposted chapters. So most of the complainers have stopped complaining and asked him to just post more often on his progress.
The author has revealed that the reason he didn't post the epilogue is that it was originally written before a change in the plot made it incompatible with the ending. No details have been revealed so far.
Word of God: The author posts on this work's discussion page.
"If there is any character in Methods who is a Self-Insert, it is Godric Gryffindor."
Hermione is, in fact, Professor McGonnagal's secret long lost great-niece. Apparently her twin sister gave birth to Hermione's squib mother at some point during the war with Grindewald and died shortly thereafter.
Write Who You Know: Much of Professor Quirrel's characterization was inspired by Yudkowsky's colleague and co-blogger Robin Hanson. The whole "being evil" part is pure fiction, though. (We hope.)