I'd take a wild guess here but I feel it has to do with a few factors.

1) He has a pretty strong back story which is something that was pretty unseen for FF villains at the time. Though it had the unfortunate implication of making players sympathize with him more than the creators intended.

2) He was an interesting take on Zemus' role in FFIV where he spent the majority of the time manipulating bodies to do his dirty work.

3) He was cool looking, I don't even care for the dumb sod but I'll admit he's got a sleek badass design that made me gravitate towards him back in the day.