I agree. Looking at her life you can feel sorry for her. Cast out by both Jedi and Sith, it really makes you feel sorry for her. She's such a great villain with real motivations. Not like Sion and Nihilus where it was like "Kill everything". While that was kind of what was going to happen with her plan, but it wasn't her intent.
Looking back at her, I gotta say that she's one of my favorite Star Wars villains.
Didn't care for Sion at all, but I loved Nihilus, primarily due to what he was in relation to Kreia's philosophies. In my eyes the game's story is about how the Force relates to our human emotions, and Nihilus plays an important role. He's not so much a person as much as a notion.