The Following content is an opinion
Do not allow it to offend or cause problems, such as flame wars. These opinions are also not the official opinions of Final Fantasy Answers, which can be taken to be a neutral point of view. The most popular villain is most assuredly Sephiroth. All villains, however, have their ups and downs: Emperor Maetus has the most power at his command, while Exdeath, Cloud of Darkness, and Yu Yevon are the most connected with a spiritual essence. Garland is the most classical; Golbez is part alien; Kuja is a being created for the sole purpose of killing. Kefka achieved the most rampant destruction; Sephiroth was created to be the perfect warrior; Ultimecia can bend time itself; Vayne is granted the power of an esper. It is all a matter of opinion who is the "strongest" though, and what your definition of "strong" is.
I'm glad you people think that way.
I guess ill pick Kefka...