A lot of Kefka's popularity can be attributed to Ted Woolsey and his liberal translations. He's the same guy responsible for FF I's "I, Garland, will knock you all down!" among many others. For better or for worse, his work actually made Kefka sound a lot cooler and creepier than he did in the JP version. There, he was just kind of a villainous jester than a full-blown psychotic clown with a nihilistic agenda.
Otherwise, I think it's not really what the goal or the actions the villains do but their motivation that sets them apart.
Take for example how Vayne Solidor and Cid turned out in FFXII. Yes, they were villains who succeeded with their plans like Kefka, but the finale reveal demonstrated that they had this general ideology of man being good and were pursuing a goal to make that ideology possible. They had a good goal but went about it using the wrong means. It's a much more relate-able villain than someone who wishes just to kill everyone or make themselves God.