Scorpius is right up there at the top of the list, I agree with that.

But I think that Londo Molari beats Scorpius as a villain because we see every step of his journey from a minor government official in a position that is regarded as a joke back home, his first grasp at real power, his gradually rising self esteem, his surprise and disgust at the bombing of Narn, his attempts to undo his mistakes without losing his new position and the respect of his peers back home, etc, etc. All of this happens gradually across the five seasons of the show.

With Scorpius we only get a single episode detailing his backstory, and he probably customized that heavily to appeal specifically to John. He does stick to his stated goals and motivation even after he loses his power base, so there was at least some truth to it, but it is still a lot thinner.

And all along his slow roll down the hill we understand more and more his patriotism and his longing for a return not only to the height of his empire but also to feeling anything other than depression, guilt, and ennui.