The greatest video game bosses, like any villain, are ones that are made and not born. I find an end boss far more engrossing if I can see what they were like before they were such a horrible fear, and Final Fantasy VI is a documentary on Kefka.
If we break down the actual gameplay, Kefka's fight isn't really phenomenal in terms of raw gameplay. What makes this fight insane is we know Kefka. You know Kefka. Think about who he was when you first saw him. A weird little jester? Almost like an Ultros? And what is he now? God. Halfway through the game, Kefka turns into God.
I'll never forget this fight simply for that weight behind it, the weight that Kefka accomplished his goal. Kefka isn't Sephiroth, a tragic mistake who just couldn't accept his faith. Nor is he an Ozma, a natural force that you were unfortunate enough to disturb. Kefka is the God of Magic, and his rule is marked by an unstable disgust for the world around him. He got his hands on the statues of the Warring Triad and made the conscious decision to plunge the world into darkness. And he started as a joke, a character who the game he is in seems to care little for.
You really can feel a sense of agency behind Kefka, almost like Lucas in Mother 3. Lucas is NOT supposed to be the protagonist of Mother 3. Flint is. All you hear about at the start of the game is how much reverence everyone in Tazmily has for Flint, similar to Ness at the start of Earthbound. But Flint isn't the protagonist. Lucas has to accept this reluctant role, one that he is very much not suited for. The game tells us as much when it calls him a crybaby at every turn. Kefka is NOT supposed to be the villain. Gestahl is. Why would it be the weird clown, right? You just never see it coming. The story is written in such a way that it feels like it was hijacked. Kefka's rise to power (at halfway through the game) is such a fantastic bait-and-switch. And having to climb that tower to get to Kefka on his throne, this Luciferian figure? There's really nothing quite like it.