Final Fantasy X-2 - It killed the good story of FFX and made this game a washy J-pop like game with a fanfic like story.
The 3rd Birthday - Oh my god the story is so terrible that the story pulled down the scores of this game.
Final Fantasy XIII - I admit the lore of this game is pretty good (because it wasn't written by Toriyama) but the way Toriyama interpreted it was terrible. The story was lacking, too much on drama, and everything was shoved to the datalog.
Final Fantasy XIII-2 - If you thought the story in FFXIII was hard to follow, what more of the sequel? This game made the entire FFXIII saga even more confusing, and FFXIII wasn't meant to be a saga from the start.
Lightning Returns: Final Fantasy XIII - The story is even worse and according to the reviews, it's underwhelming and lackluster.
Dissidia: Final Fantasy - From what I've played the story made no sense. Sure it's a fighter and the story isn't the focus but the story still doesn't make a lick sense.
Front Mission: Evolved - I know nothing about the story but according to Femmeworth: really fucking bad