I ain't choosing a main villain, cuz frankly, the majority of them are boring dreck. Top three:
1) Rubicante:
Playing FF2/4 back in the day, it kinda blew my mind that here was this big-time villain who actually
went out of his way to restore you to full strength before the big fight. Honor in RPG villains wasn't something I was acclimated to, not back then. Still a total boss in my book.
2) Ultros:
Nuff said. (As an aside, his voice and mannerism in the English language World of Final Fantasy was what I'd always imagined him to be like.)
3) Zorn & Thorn:
These two were a constant, well, thorn in your side for a large portion of the game, that I was just itching -- nay,
praying -- to have a proper showdown with them. Their fused form is nightmare-inducing. (Also, they've got
an amazing music theme.)