In my opinion, Ultimecia had the best exit for a main villain because she was able to cause a time loop in her ominous final scene.

The way that she passed her powers onto Edea at the end of the game showed that the power of a Sorceress is fearsome and cannot be controlled even by the heroes; furthermore, a sense of foreboding still remains after the defeat of the final villain and that is rarely seen in Final Fantasy games as they typically favor an absolute and hopeful ending.