I think that this lack of polarity is something sorely lacking in most YA books, and many adult ones too. There is (nearly) always a villain, and they are (nearly) always bad. Here, there were many potential "villains" other than Prentiss, and all of them have redeeming qualities - or at least, the conviction that they are doing the right thing even though their methods are wrong. Even the Mayor was not pure evil, though I will confess I hated him passionately. Nonetheless there were moments where I felt for him, even understood where he was coming from (though these moments were few and far between).
I think the reason I liked this series so much is that it shows the futility of war, as well as how easy it is to vilify people for being different. I can see how there are people that this would not appeal to but I do think that these books are essential reading, I will definitely recommend them to people in the hope that they take something good from them.