Kefka of Final Fantasy VI (III in it's American SNES release) and Sephiroth of Final Fantasy VII are considered the two greatest Final Fantasy villains. Fans often fight over which of them is better, but I've never seen anyone become a close third contender. There are plenty other antagonists who are interesting enough to serve their purpose, but no others achieve true greatness.
It's no coincidence in my mind that those two games are also popularly considered the two best Final Fantasy games. A great story needs a great villain, and a great game (especially an RPG) needs a great story.
Out of 13 games, none of which have bad stories, (sometimes game-play to complain about, but no bad stories), why are these two villains by far the best? They are very different from each other, and most of what they can be argued to have in common applies to plenty other FF villains, being powerful mentally unstable black mages with a God Complex.
I think the notable common denominator isn't between the characters but in how they relate to the story.
Both those games are the only Final Fantasy games where the Finale Boss was also the main recurring antagonist through out the game's narrative. Most Final Fantasy games the Final Boss is some Lovecraftian horror that is unleashed at the end, or an Orcus on his throne type mentioned but never met till the end. Which is the trend for JRPGs in general.
Doing that hurts the ability of any of the villains to really become a compelling character. If the climatic battle of the game feels disconnected from the earlier adventures, it hurts the symmetry of the game.
And I think it at least subconsciously effects how the writers write the story/characters. If none of the recurring antagonists are the actual main villain, then the writers may feel they don't need to put in as much effort into defining them.
The only other main series Final Fantasy game that is even close to being an exception to this is XII. That one does have a trio of interesting villains. But the actual most powerful one gets the least development.
Final Fantasy X and XIII are the most ambitious stories in their high concepts, and have an interesting cast of protagonists. But their main antagonists mostly just seem annoying, and the final bosses lacking in personality.