I think that, given enough thinking and research, you can justify almost all the FF Villains actions to be translated as... not villainous. Seymour, to me, is definitely the main "villain" because he is the one you're fighting the whole game. You can call him a victim, you can call it a conflict on interest, but that won't change the fact that Seymour is the one standing in the way of the game's protagonists.

In the strict sense of following the persective of Tidus and Friends, I don't see how that can be seen any other way. Once you move beyond that, to the Yu Yevon Yunalesca thing... lol I don't know.