I adore the moral ambiguity.
We had an outright evil human leader in Admiral Cain who essentially turned Battlestar Pegasus into a pirate ship with a vicious, brutalized crew.
I agree, it's good in the sense that it forces the viewer to think for himself, instead of the way most shows practically come out and tell you right up front whom you're supposed to sympathize with and whom you're supposed to hate. Admiral Cain did some downright ugly things for which she deserved to die, but she also had a dogged commitment that I had to grudgingly respect. If it weren't for her, her ship and crew probably wouldn't have survived all that time.
Another thing about the show that really keeps my interest is the way their society so closely parallels ours, even in all but a very small number of areas of technology. It's hardly realistic, I agree, but I'm willing to forgive it as a form of artistic license, because it's the only scifi show I've seen that actually makes space seem so accessible. And we're not that far from the point (here in our own society, that is) where space tourism can become a regular thing, and once that happens, it can become cheaper and even more accessible as time goes on.