Its funny because honestly I considered the Zilart Brothers at first to be crazy however, they successful founded and ran the major hub of Vana'diel, not to mention it was them who honestly unified the other nations, albeit it was for their own gains, but that alone gives more to the scheming arch-type of villainy than that of the crazy one. Vayne from XII was very...excessive and thorough when it came to climbing ranks and ensuring his power, which to me also gives a scheming super-villain arch-type. He was in control and a had a clear plan; crazy villains tend to not really have a plan besides "I'mma kill you".
I agree that both those characters were 'crazy' at the end but that doesn't really constitute them being crazy villains, it just means that they became desperate (most villains in entertainment medias toward the end tend to exhibit crazy behaviors but that doesn't make them a crazy villain per say)
So you are taking about RPGs in general. Well the genre Role Playing Game is pretty vague... I mean technically role playing games are identified by any game wherein you are placing into the shoes of another person (to play a role, or role play). So we can use the 3874 PS2 games as a loose point, we know that there are sports titles to rule out (soccer, golf, baseball, basketball, football, tennis, hockey, boxing, wrestling, racing), PS2 had new games being released for 10 years from its launch which means that 100 sports titles were launched, but they have competitors so give or take 300 'sports' genre titles launched in the 10 year cycle. That means roughly 3574 games can be considered RPGs (shooters are a RPG as you fill the role of a person, which is why I even listed villains from shooters in my OP). I assume you mean "over half of the titles have crazy villains" when you say its been played to death and back again so that means you are claiming that with just the PS2 games alone that at least 1787 PS2 games contain crazy villains, but since its been played to death and back I assume you mean 75% roughly of the games contain these types of villains so roughly 2680 of the 3574 RPG type games contain crazy villains? I kind of doubt that.