Emerald, I think, was one of the easiest. Just limit the materia you equip and go nuts on him. Penance, if you know what you're doing is predictable and more annoying than hard.

I still think that Omega Weapon in FFVIII is the hardest superboss. But yet again, if you have a strategy and the right items beforehand, there's not much problem.

Summarising, superbosses are only hard if you're unprepared. You said so yourself. Are you suggesting that we run in to beat Omega without junctions? Or take on Penance without Break HP limit? 'Course not.