Sin is the main villain of FFX, Seymour is just a pain in the ass the entire time, he isn't the main villain. That's like saying Jesse and James from Pokemon are the main villains, when they're only reoccurring.
Yu Yevon being the most mediocre boss I've fought in years does NOT deserve the title of main villain. I don't care if he really is, he does not deserve it! (SPOILER)Well really Jecht (bleh Final Aeon whatever) was the last boss of FFX and yu yevon was just for closure and story. So his appearance in Dissidia is justified in that sense.