Sophie Pathos isn't too bad, especially if you bothered to finish the Robot Professor side quest

Personally, I felt the Space Pope in Episode II was longer but that whole battle system dragged out every encounter unnecessarily. Episode III also had that long ass battle with Margulis in his E.S. Still, it was a damn fine series.

As for Nyx Avatar, it is pretty long, especially when the boss decided to Charm Yukari and have her cast her best healing spell and restore all her health. Course, that is when Messiah is useful cause if the boss decides to be cheap, so should you.

The final boss battle in Legend of Dragoon was also terribly long and got pretty boring. Especially since the game hands your main character Godhood right before it.

I still haven't beat Yiazmat and have not even bothered to try out Omega mk. XII in FFXII. I simply gave up out of sheer boredom cause it was five hours of the same bull. He's not incredibly difficult but he is boring to fight with or without Gambits.