>>58103459Ghetsis, because he's smart and knows the gravity and implications of his ambitions, and genuinely would have succeeded if the player didn't have plot armor he was that close to victory. He frames himself as a benevolent god-emperor and Team Plasma as a noble and just organization, and both civilians and grunts actually believe it because he isn't the type of bad guy who's explicit about being a super mega evil ecoterrorist trying to enslave a god and kill everyone.
He's maniacal, he's insane, he's a narcissist, he's a psychopath and he can put up a very convincing front to hide it all completely. Ghetsis' actions throughout the courses of BW/B2W2 explicitly affect the region more than once, and he's such a persistent threat so set in his goals that it takes the player pushing him to his absolute mental limit to get him to bring about his own downfall. It's only truly over once he gets completely mindbroken into placidity and is no longer a threat, at which point he gets escorted off to an asylum to spend the rest of his life.
>TL;DR Ghetsis is a good villain because you cannot "win" against him no matter what, the only way to actually defeat him is to get him to defeat himself. Also he tries to kill you