I never had much trouble with most of the main story bosses. But I enjoyed being able to go on quests that would be very challenging for my party's levels. Right after doing the first Gilgamesh hunt I went after him for the second round and got my ass handed to me because he went up like 15 levels. I barely managed to defeat him the 2nd or 3rd try.

Overall, I approved of the game's difficulty. There were a couple of story bosses that were difficult/annoying (Elder Wyrm), and regardless of how leveled you were you could easily take up challenging hunts. The significant number of hunts is a good way to keep things interesting for any playthrough (the other being having enemies/bosses level up with you).