FFX. Not Yu Yevon - I don't consider that a final boss so much as an interactive epilogue battle, ala Shirtless Sephiroth. No, I'm talking about Final Aeon Jecht. Sure, he *looked* nice, and it made sense as a fight, but they just tossed in that obnoxious Otherworld music. I mean... it's the final boss, at least remix it instead of using the exact same music as the intro scene of the game! gonk
...Of course, if nitpicks about soundtrack choice don't count as a valid complaint, then I'll go with Necron of IX. You beat Kuja, think you've won the game and then SUDDENLY there's a new evil mastermind. He wasn't even loosely related to the story, he just - and I paraphrase here - walks up to you and says "Oh! Hi! I was watching you guys fighting, and it made me a bit depressed about the state of the universe. I think I'm going to destroy it now. Ok, bye~!"
He wasn't even as visually impressive as Kuja tossing out his Ultima variations. If you're going to steal the spotlight at the last minute, at least do it in a stylish, awe-inspiring manner. emo
EDIT: Special mention for Zeromus. That was just silly. sweatdrop