Lots.
Final Fantasy XIII. Orphan form one and the dude before him were harder then Orpan form 2.
Prototype. Elizabeth Green was much fucking harder then the Supreme Hunter final boss. (I believe he was supposed to be called the Supreme Hybrid since you already killed a Supreme Hunter. Plus the achievement for killing him said Supreme Hybrid)
ReservoirAngel said:
I'll point to Final Fantasy X. Any of the bosses is more difficult than Yu fucking Yevon, a boss you could kill with a rolled up magazine or a can of bug spray.
I don't think you can find a more pathetic example of a final boss in any game.
That battle was supposed to be more emotional then challenging.
I would also like to bring up Superbosses.
The WEAPONS in FFVII
Yaizmat, Zodiark, Hell wyrm were all harder then the Undying in FFXII
Mobius 1 in Ace Combat Zero