I like stories that don't have definite good guys and bad guys. Life isn't really made up of people who are either good or bad, but rather of complex people, all of whom have value. One part of Middlesex that I liked was that the physician and the religious guy were the two (almost) scummiest characters in the book. I like being a physician and a religious guy, and I can't help but believe that I choose those parts of my character because I think they are good. It's a nice reminder that they aren't necessarily good.
On the other hand, I do get a little annoyed when there are no contrasting characters to give a little balance. In contrast to Dr. Luce was Dr. Philobosian, a great doctor. But where was the parallel character to Father Mike? I don't remember one. He was just the villain of the book and, in this tale of sexual ambiguity that already has plenty of spiritual controversy built in, we'll make him the ultimate antagonist as well. Did anyone else catch the filthy description of the baptismal font? The slimy water with a band-aid in it? Sounds like hepatitis waiting to happen. Oh, and tricknology? That's the view of religion I got from the book, and it's one of the very few complaints I have. I'm not against religious villains, but I am against the next step in which it gets to be too categorical.