That I read books one and two in one morning show that they really should have, at least, been one book together, but I already bitched about that in my review for part one.
Anyway, DC's publishing choices aside, this was a very good story. Batman's never been my favorite character, but he's very interesting when done right, and his rogues' gallery is classic--they are very prominently featured here. Almost all of them. (Although, it would have made some parts of the plot work a little better if the Mad Hatter had been included, in my opinion.)
Jeph Loeb seems to really love writing mysteries, which is, of course, a natural fit for Batman. This one twists and turns interminably (in a good way) and while I guessed the biggest part of it fairly early on, I not only got the details wrong, but was still entirely surprised by the very end itself. More importantly, though, then if the mystery worked was the characterization, as this story was clearly written with the understanding that it would be a "MAJOR" Batman story from the get-go. It is always when Batman's personality is really being explored that he's at his best (because his personality is seriously messed up).
Also, Jeph Loeb is good at writing for his artists, and he gives Jim Lee a good deal to work with here. Lee himself, seems back to being more restrained than he was, say, in the early 90's, and the book definitely looks great.
Can't really go on without spoilers, but a good read. Borrow them or buy them used, though, there is no good reason a 12-issue story should be split between two books.