It's a tie for me. Both of mine are from the Star Ocean universe.
Indalecio (aka Gabriel). He's 4 billion years old, intends to destroy the entire universe, and has the power to do so. The only reason that didn't happen was the fact that he intentionally held himself back to give the universe a fighting chance.
I never managed to take him down with his limiter off (although to be fair I didn't have my party at the max possible level in the game because that level was 255 and I CBA). You had the option to make him "limit" himself, which made the fight considerably easier. If you didn't use that option, he was far more difficult.
Ethereal Queen
She is also pretty mean. I don't know as much about her story, but in terms of game mechanics, she's one of the hardest bosses I've ever faced. She views you as inferior and offers you a servant position when you encounter her. If you turn that offer down, she opens a can of whoopass on you. She's pretty equal to Indalecio in terms of difficulty.