OMG YES. That's one of the things that FF and even Mario games have that Zelda doesn't: superbosses. If I have to count up the ones I can remember:
All Pit of 100 Trails type bosses of Paper Mario TTYD/Super Paper Mario
Emerald Weapon and all variants (FF7)
Zodiark (FFXII)
Ultima (FFXII)
Hell Wyrm (FFXII)
Yiazmat (FFXII)
Omega Mark XII (FFXII)
Vercingetorix (FFXIII)
Long Gui (FFXIII)
Lightning [IIRC; I know she's DLC in the arena but dunno if she's OP] (FFXIII-2)
Omega (FFXIII-2)
Gabriel Celeste [or Celesta] (all of Star Ocean, especially SO3 and SO4)
Lenneth (SO3)
Freya (SO3)
Iseria Queen/Ethereal Queen (all of Star Ocean, especially SO4)
All of Wandering Dungeon and Cave of Seven Stars bosses, even with high end Laser Suits, Laser Weapons, LV255 all BT stats (SO4)
All of the above bosses range from moderately to extremely difficult. Zelda has nothing like this (though personally I'd say that Trinexx from ALttP could be a superboss had it far more HP and attack power, and all of AoL is pretty much a superboss in and of itself). Implementing superbosses through post game content is easily a win win situation as post game content is entirely optional by definition, it doesn't get in the way and can only make a player enjoy the game. Even the likes of Sphere 211 (SO3) can make a Zelda player happy [I konw because I AM a Zelda player]. No matter what way you slice it, superbosses fits into the Zelda equation because they're just optional, amazingly difficult bosses that enhance enjoyment. They're not forced encounters, therefore complaining is invalid as far as "OMG TOO HARD". Too hard is the definition of superboss.