I've heard the Demi-Fiend boss fight in Digital Devil Saga is one of the hardest battles in RPGs. Not only does he utilize the typical MegaTen rules like later bosses Elizabeth and Margaret, unlike them, he doesn't completely stick to a set pattern and he has a game ending move he can use whenever he feels like. Now someone did finally come up with a strategy that beats him pretty easily by cheesing the system a bit but apparently trying to beat him without said strategy requires some serious strategizing.

Honestly, pick a MegaTen super boss, any of them, still found them easy, try fighting them on hard mode.

The final boss of Star Ocean 2 without his limiter is also a serious pain in the ass whom most strategies I've read involved farming battles with the games resident super boss just to max out your levels in order to stand a chance against this asshole.

Bosses that should get more respect are the Divinegon from DQIII remakes or the Egg Dragon from Lufia 2. Beating them isn't difficult but each time you beat them, you get to choose a treasure. In order to get the rest, you have to fight them again and beat them in less turns than the last time, making getting all the treasures from them very difficult as the fight gets harder each time.