This is a really good story. Confusing in a couple of parts, but really good none-the-less. I would like to see more heat between Harry & Hermione (go to http://fanfiction.portkey.org/story/6612 to see what I mean by that..).
I also really liked the character development that you've done. If anything, that's the strongest part of the story. I'm not sure how the plot itself hangs together, but the characters (flaws and all) are really strong & I think you've done an amazing job with Hermione. You've got her nailed down very, very well. I also think that you 've done a nice job portraying Ron - with all of his weaknesses, etc. The character that I think you'd been less than kind to is Minerva McGonagall. She's kinder to Harry than you've let on.
Anyway - pls. keep writing!