I just want to point out that I didn't technically say Yu Yevon was evil. However his main purpose is that he could keep summoning Dream Zanarkand, and to do so he needs to keep Sin and the Fayth from dying permanently. This also means that he would possess any Aeon and use it as a last resort against anyone or anything against Sin, hence the reason he possessed the Final Aeon as well as the rest of the Aeons near the end. Technically, HE isn't evil, but the things that he does for the sake of his dream are considered evil, and despite that he was the largest threat, as he maintained Sin devastating Spira for many years.
I want to think of the "main villain" as the biggest threat in a game and not the most malicious person.