It's not a game for everyone. It makes no pretenses for being a game where there is always a good choice, and I find it refreshing. At its core it's an adult game. Not like how Mass Effect is an adult game- it's more of a teenager's view of what adulthood is like- instead it says, here's a fucked up world, you're a guy that everyone hates because they're superstitious/power hungry and you're a abnormality that can severly change the power balance in a kingdom. Go.
Honestly, I got it a few years ago, when I was in high school, and I really couldn't get into it. I just played it again recently- my first complete playthrough of the game- and I found I really enjoyed it. Maybe it's because I've actually gotten some experience outside of a scholarly institution, I don't know. I just found that the fact that there was no 'good' or 'evil' option in any of the choices was great, it's just a choice. And I think that's the thing that drives the most people away, the fact that there is no defined 'good' or 'evil' choice is something that a lot of people can't get into- compared to something like, again Mass Effect, where you have defined good and evil choices, where even the most grey choice is along the lines of kick the puppy eat the puppy alive.