Hardest for me had to be Proto Babil. After beating the game for the 2nd time not too long ago and had realizing I was able to fight him, I gave him a shot. All of my party members were lv. 99, and yet there are still certain abilities/equipment your characters have to have to make this battle less stressful - even at the highest level. Took me a good 12 minutes to finally beat him .