Bahamut states within the game that Yu-Yevon is neither good nor evil (the nature of his appearance during the Final Battle only seems to confirm this), which makes him unable to gain the title of 'villain'.

While Seymour believes that what he is ultimately what is best for Spira, his methods of achieving his ends in addition to the sadistic glee he takes in accomplishing them (for reference, his conversation with Kimahri before the third battle with him) definitely makes him an villainous character.

But yeah, I wouldn't really call him a bad villain, even if his role in the plot is only equivalent to that of the supporting antagonists in other titles.