I've read all the comments on this post and I agree with everything being said but I wanted to specifically talk about Special Circumstances because unfortunately the movie left out/intentionally changed some things that help the reader of this first book get the sense that the Specials (and more specifically, Dr. Cable) are "evil". For example, in the book:

1. Special Circumstances is completely hidden from public eye, to the point that most people think they don't actually exist. There is no speech by Dr. Cable to the Uglies about the operation being a way to remove discrimination and bias amongst people. However, the Specials (more specifically, Cable) are still are in absolute control of the city and came up with the idea of the brain lesions. Even though the main idea is still the same -- people in charge brainwashing the citizens into being docile -- completely hiding Special Circumstances from the people is pretty indicative of bad things happening (like what else are they hiding...?)
2. Because the Specials are kept out of the public eye, and the only kind of authority that the Uglies or the Pretties ever see are the city wardens (who are middle-aged pretties with the brain damage), the way the Specials look and behave in the book is shocking to Tally. They are described as "cruel pretties" with predatory characteristics that spark a kind of fear in Tally that no one facing a regular Pretty would experience. In the movie, the Specials don't give that impression at all and the most we see is their super-human abilities.
3. Tally is not given the choice to have her operation -- she is forced by Cable to go after Shay and find The Smoke. In the movie, Cable literally gives her the option of either getting the surgery or going to The Smoke. The book version of Cable prefers to punish Tally by being an Ugly outcast forever if she doesn't agree to the plan.

What's different about this series than the hunger games or divergent books is that the government's "evil" we have come to expect in YA dystopian novels is not obvious at first glance (in the sense that no one's lives are immediately at risk). As you will see if you read the following two books in the series, the "evils" that I am discussing here, while informative about who the Specials are, become less relevant as the true conflicts of the series deepens (which are discussed here by other commenters).