I believe the hardest optional boss in the U.S version is Nemesis. I've never fought it before so I can't really say how tough it is to fight Nemesis.

For storyline bosses I would have to say that the Sanctuary Keeper was pretty difficult during my second play-through. My second time through the game I didn't over-power myself at all. The Spectral Keeper can be difficult but probably more time consuming with the mechanics of the fight. Yunalesca can be irksome if the player fails to realize that at least one character must have the "zombie" status when she goes into her third form and to at least have 1 character zombie'd throughout the rest of that fight. Braska's Final Aeon also gave me some trouble in my second run of the game. I had to acquire "Quick Hit" for a few characters in order to help me out in that battle.

I would say the hardest would either be between: the Sanctuary Keeper or Braska's Final Aeon.