I will agree I like Sephiroth's story, it's his character that does nothing for me.

And I don't mind if the villain is revealed a bit later, (At least by the 70% Mark usually. ) but ther are acceptions to that, one of which I'll get to eventually. ;P

And I can think of very few main villains which are NOT involved in most of, if not all, the games plot. It just depends on when you run into them. ;P