For me, the problem with Bag of Bones is that, once you look back on it after reading it, it doesn't amount to a whole lot. In the end, it is a simple urban legend, almost. The same thing happened to me after I read Duma Key -- it was a lot of writing supporting too simple a concept. Juxtapose these books with something like It; after you read It, you don't soon forget it (or It, for that matter). It's been a while since I've read Bones, but I seem to recall a character in there that I thought was going to turn out to be a witch, but didn't; if my memory serves, my confusion may have come from the dust-jacket description. Now that would have been cool.
Going back to Duma Key, for a second, I have to say that the book begged to be written in the third person. That might have made it more substantial. But in the end, both Bones and Key lacked the profundity of an It, and probably should have existed as works with a significantly smaller amount of letters.