The end of FFXIII-2. Fuck you, Square Enix.
I would also have to agree about FFIX. The whole Necron shit made me lolwut.
Also, FFXII. Not so much the story, just people's motivation to even be a part of it in general. Especially Vaan. "LOL I WANT TO BE A SKY PIRATE" doesn't cut it as a reason for the entire game.