Jecht wasnt really the "villian" at least story wise, I think for whatever reason square really just wanted to push the whole father/son bitchfest relationship between tidus and jecht, so they made Jecht the penultimate story boss. They seemed to kinda tack the whole yu yevon thing on simply to give sin and yevon some sort of origin. But as this thread mentions its a tenous origin at best, pushed into the background in favour of focusing on tidus/jecht whingefest.
( I love ffx, am replaying it now, but tidus as a character is really annoying, mostly with the whole, "my dad was a bit mean boohoo story")
Does this help?