Heard that one before?
It's interesting to me that in both Final Fantasy III and Secret of Mana, that the emperor is almost a non-Character. We hear about him, but the real villain with a fully fleshed-out personality is one of his aids (Kefka or Thanatos). These aids treacherously overthrow their master and then get down to the business of doing some real damage.
Why is this?
One could see this as a reflection of Japan's World War II experience where Emperor Hirohito got a pass while Tojo took the blame. It could also be that an Emperor is essentially a glorified bureaucrat and that makes him relatively uninteresting as a video game villain. An aid, or a right-hand man can mix it up with the heroes on a man-to-man basis with greater credibility. Finally, allowing the aid to over-throw his master shows the player just how evil and ruthless the villain is. After all, isn't there supposed to be honor among thieves?
Of course, these answers may be wide of the mark. Still, it seems worthwhile to ask the question: "what does make for a good villain?" Is he someone who starts off with power and position, or is he the anti-hero, going on his own twisted hero's journey?