Depends on what you mean by danger. Destroying the world the characters are on? or seizing control of the peoples lives/fates. Kefka and Sephiroth are the former, Seymour would be like the latter. Depends on what logic you are running on.Which Final Fantasy games do you guys think had the greatest sense of danger all throughout, while playing?
Kefka and Sephiroth are just insane.
Seymour would be the more insidious one to me. Considering his position of power and the means he uses to gain it. Yu Yevon by that point was no longer human, he was just a machine. Arden comes under "tragic Villain". Motivations for the villains widely differ. Ultimecia to me would be the most selfish. Time Kompression was her way of making herself be alone, all powerful but alone.
Kuja's fear of death made him the person he was, that combined with Jealousy over Zidane being the real angel of death from Terra.
Sense of danger depends on what you fear about these Villains. The ones i have not mentioned all have their reasons.