All-time hardest boss... New-school, anyway, I have to go with both Mach Jentra and Great Redips in Megaman X Command Mission.
Jentra, at the level I fought him, was so very, very frustrating... He's FAST, and he's a TANK. The second time you fight him (Late in the game, like every other Mega Man game in existance, duh), he's hella-easy. It's embarassing, really.
Great Redips. Oh dear GOD. Between his Momemto Moria (Inflicts EVERY status effect on the party all at once) and his Carpe Diem (Depletes all of the party's Weapon Energy/MP), he was really annoying. Not HARD. Just frustrating.
Just say you get up to 90% Weapon Energy with X. Great! Next round, he'll be at 100%, and you can shift into the X-Fire hyper mode and whack him with a Charge Collider for STUPID amounts of damage.
BAM. Carpe Diem, buddy. NO W.E. FOR YOU!
I don't like that guy one little bit.
But perhaps the most frustrating part about MMXCM is ... NO NEWGAME+!
I am sad.