I never understood why there was so much Cassie hating!! Cassie was one of my favorite characters growing up, and even more so now as an adult. I think her constant search for some kind of moral peace with everything that she had to do was far more interesting and relatable than, for example, Rachel's blind bloodthirstiness. I think many readers liked Rachel so much (and Marco for that matter) because we all secretly wish that how we would be able to be life threatening, war-like situations; brave, efficient and unemotional. When in fact, most of us would have had the kind of internal struggles Cassie often voiced. That being said, I guess characters like Rachel and Marco are more fun to read.
But I totally agree that she had the potential to have a dark, manipulative side. Though I think we had enough darkness with Rachel, especially towards the end there.