In some regards this comes down to a matter of how you define “villain.” Not to sound esoteric, but it is exceedingly easy to weigh the various candidates to quite different standards. That having been said, the extra detail of “greatest, most successful” villain gives us a clear indication of the direction in which the topic creator desires this move forward. In other words, irrespective of our personal concept of what makes a villain, he’s asking the slightly different question of who was the best at it. Therefore, without offering my own definition of what a villain actually is, I’ll talk about who I think did the best job of it in the SE universe—or, rather, just the S universe, because I don’t think I’ve ever played any games from predecessor Enix.
I admit to a soft spot for evil characters in video games. Sometimes they are far more interesting, more intelligent, more ambitious, and more direct than their counterparts, and with their audacious plots they are singularly responsible for creating the entire story. Their fatal flaw is that they are always weighed down by the game writers with negative characteristics that inevitably cause them to lose in the end: shortsightedness, excessive cruelty, hubris, etc. Were these gratuitous failings swept clean of their charsheets, many of these villains would actually be closer to my personal definition of “hero,” inasmuch as I acknowledge the word at all, than the official, playable heroes.
Gestahl did a good job of being a villain, ruling the Empire for a long time, making it prosperous, succeeding in his conquests, and pursuing a singular plot to attain supreme magical power. He only failed by growing drunk on his power toward the end—and even then he might still have succeeded, were it not for the deus ex machine of him standing in the wrong place at the pivotal moment. Gestahl desired order and had a mindset decidedly more constructive than destructive. His vision of a world where the Empire was truly supreme is, perhaps, something to which many of us can relate when we reflect upon our own wishes for an ideal society. The fact that his top general, top scientist, and top Magitek Knight were all decent people also says something about the quality of his reign and administration. It is easy to look at the Empire as a symbol of depravity, corruption, and industrial decay…but these images, borrowed from the Japanese ethos, were the mark of every industrial society at the turn of the twentieth century…right down to the bawdy soldiers in the lower ranks of the military. The Empire was a much more realistic aspect of FF VI than we give it credit for, in whose absence the game would have been considerably less historic. I would therefore rate Gestahl as a very successful villain. Had he been more disciplined and less compulsive as his plot was finally coming to fruition, he might have gotten exactly what he wanted.
Magus was another successful villain. In fact, he did achieve his ambition, by allying with Crono & Co. and building a rapport with them—without ever truly becoming one of the good guys. In so doing, he also escaped any punishment for his considerable villainy, left an entire continent to wipe up from the aftermath of a long war, and singularly escaped the terrible fates of his entire family and Kingdom. So, for the price of some emotional scarring and the particularly painful lost of his sister, Magus succeeded about as wildly as any villain in a video game could ever hope.
Ack! The hour grows late, so I’ll cut it short here. I think I’ve gotten my point across. I do, however, want to throw in a (modest) word of support for Marche, for the reasons laid out already.