Usually if I find a boss hard it's because of some damn ranking requirement. So far as just beating the boss goes, I can't possibly post anything that compares to Vix's bullet storm from last page, but nevertheless I'm surprised nobody mentioned this yet:
-Chornoforce, Hard Mode, ZX Advent.
Narrow safe zones combined with a constant time bomb, yeilds a character who is hellishly tough at ANY point in your typical Inti-crippled Hard Mode, much less having to fight him as your second or third Pseudoroid of the game.
And one other one, that actually isn't as tough as getting to him, but still memorably difficult:
-Mysterial, Pokemon Battle Revolution, Masters Final Set (Diamond version linked with the game)
They finally did it. They finally put a Choice Scarfed Kyogre on the CPU's side. Good luck.
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)