Perfect example comes from KOTOR 2. Look at Kreia. She was a phenomenal character because her power wasn't insisted on - she herself spent the entire game intentionally avoiding the limelight, then BAM. Suddenly you have to kill her.
Granted Obsidian did a poor job in areas with TSL's writing and cutscenes, but she is easily the most compelling Darksider I've seen to come out of the EU in recent memory.
Though I can't ever bring myself to like Malgus because...well, let's face it, he's Malak 2.0 without the cool deathscene and Star Forge MacGuffin.
That's your opinion, and that's completely fine. I personally like Malgus myself having read his novel and so forth, but I think we can both agree that Malgus by comparison to his boss, was a far more effective villain. You felt his presence and the chill of evil with him throughout the game far more than you did the Emperor, even in the JK class story.
But you hit the nails in the head there my friend