I'm actually quite surprised that there are people who consider Kuja 'less' of a memorable/great 'villain' than other great ff villains.
Yes, he wasn't 'scary' (I remember my heart pounding in my chest when I went after Sephy or Edea), nor was he irritating like Kefka (in a good way, it made me really want to kick that guy's ass ^^')
Each memorable 'baddy' in the ff series is very much the same as the others, but at the same time unique.

Kefka- scary, yet so irritating that I didn't care and wanted to make him face the music
Sephy- intriguing, mysterious, scary, doing the wrong thing without deliberately doing 'the wrong thing' (yes, this sounds weird, it's just mho)
Edea- See Sephy, yet she just seemed bored most of the time (which somehow added to her character)
Kuja- Made me go 'Kujaaaaaaa' every time he came about; mysterious and intriguing, yet he was also witty and one of the most intelligent ff baddies around (and that's saying something)