My favorite aspects of this book are the characterizations of the two protagonists especially (Sophie and Agatha) and the way the story deconstructs the good vs evil dichotomy found in fairy tales. I'm less impressed with the execution of the storytelling in some areas--there are moments that are dramatic that don't feel very dramatic; they're rushed over. Pacing is maybe the biggest issue. Sometimes as a result I'd be confused about what was going on. Other times things feel belabored because you're far ahead of the characters.
By the end there were enough surprises, layers, and bucking of conventions to win me over. Just as I'd think the story was heading back into black and white, good versus evil territory, it would reveal an interesting new way of looking at a fairy tale world (i.e. our world, really). In that way it follows through on something Harry Potter raised but didn't ultimately challenge with the Sorting Hat business; that we don't "sort" into one thing or the other easily.
There's some great challenging or play with gender roles and even sexuality. The world has a lot going on, though like the pacing, it can feel rushed (it was hard for me to separate the teachers from one another and many of the lesser characters on both sides). I'm guessing the next book(s) will continue to flesh out this world, and I'm looking forward to it!