Note: There’s a good chance this topic will be spoiler heavy and even if it isn’t then the following message still contains quite a bit of them.
My favorite is Seymour, yes, you read that right. His whole scheme was actually somewhat original, and he also appears
to be one of the most cunning villains in Squaresoft history. Sure, he’s not the most alluring character out there
which seems to be the main deciding point when it comes down to whether people like a character or not... but he
actually had a reason for doing what he did; he believed it was the correct thing. Kefka was significantly insane and
all but he really didn’t have much of a motive behind his actions. (Although, I like Kefka so don’t get the wrong
impression there.) My second favorite would be X-Death, and that’s only because he actually required a bit of strategy
to beat, or at least at the level I was at. I greatly like strategic battles.
Now before there are a million replies stating “Sephiroth!!!11onehundredandeleven11” I must make note of something here; there’s a good chance JENVOA is actually the main villain in FFVII and that Sephiroth died before the game started. As we see within the game, JENOVA can completely take over the mind of a person when they let their emotions get the better of them. Sephiroth was incredibly shocked at finding out he was merged with other cells just because Hojo wished to experiment on living creatures. Note here that the rest of Shin-ra did not know of this. Either way, the result of finding out the reason behind his strength had a negative effect and thus weakened him to the JENOVA cells in his body. Sephiroth had a lot more JENOVA cells than Cloud yet even Cloud almost killed Aerith and gave up the black materia while under JENOVA’s control. It was more than likely that JENOVA is what burned down that town, and later we see Cloud’s sword go right through Sephiroth’s body and then toss him down. President Shinra, Aerith, and Tseng all died from blows weaker than that and thus comes the conclusion that Sephiroth’s human cells died right then and his body is JENOVA’s mindless puppet forever more. Of course, you’re free to differ with this and still say Sephiroth even if I fail to see how he’s a villain.