To me, it's many but these are the hardest 2D fighting game bosses that I fought:
-First off, it's Gill like everyone said. He does not spam as much as other 2D bosses but he just fights with finesse
and even say god-like comments when you lose against him. His "Resurrection" is annoying!
-Second off, it's Shin Akuma on CVS 2. He pretty much spams double air Hadoukens and Hurricane Kicks with a Shoryuken by the end that can take over 1/3 of your life.
When he does the 33-hit Shun Goku Satsu, my jaw just HIT THE FLOOR
-Third, I-No on Guilty Gear X2. She pretty much use the move with projectiles flowing around the entire screen that will annihilate 1/2 of your life when you get caught by them
-Fourth, Onslaught on Marvel vs. Capcom. He always interrupt my combos and supers by shooting a big ass beam, Magnetic Shockwave/Tempest, or just charge towards you!!
He even regenerate
his life when he summons a clone of other playable characters!
-Last but not least, Magaki from KOF XI.
He keeps shooting projectiles that randomly flows around the screen and when you get close to him, he will shoot a barrier that deflects you back away from him. He even unpredictably
dish out a super that covers the entire screen!!
-If Magaki is not enough, Saiki in KOF XIII will throw you once you're close to him, or else he will shoot an unblockable projectile.