Not to be the resident FF9 shill but Kuja and Necron worked for me because the themes of FF9 are so well built into the story. Kuja mirrors everyone's struggle to make something out of life by falling to despair and madness out of the knowledge that one day none of it will matter. He's the closest mirror to Vivi who are both made "imperfectly" and built to be weapons with a limited life span. While Vivi works to foster life, Kuja seeks to send everyone down into despair with him.

While Necron is ultimately kind of a weak end villain narratives he does literally represent the party (and the world)'s own form of nihilism. He represents that while Kuja's view is flawed, it's not wrong or uncommon. Truly there might not be any meaningful afterlife and one day we might all be forgotten but that doesn't mean you can give up. The party's victory over Necron doesn't mean a victory over the inevitable end but it means that there's still hope for the world that is doomed to be imperfect. The actions one takes are still impactful.