Yeah, I see what you mean. I once knew a guy that was in love with Rufus, and was in denial of his death!
You know, I'd never seen it that way, but yeah, you're absolutely right - and yeah, he and Rufus are really great villains. Final Fantasy has some of the greatest and some of the lamest villains ever. Still, though, I think none of the FF villains can Outshine Kefka. The "Light of Judgement" was just too cool. Is it me, though, or was there a huge Star Wars undertone in most of FF6? You know who one of the coolest villains ever written for a game was, that I just remembered? Yellow 13, from Ace Combat 4. He's presented in a very different way from how all other villains are - and you learn about him being a father-figure for the protagonist of the "graphic novel" part; and then there's that whole issue with Yellow 2... you get to almost care about the guy, even if he does happen to be one of the damn Erusian fascists...