Gummi ships sucked in KH1 but I felt the second game did a stand up job and made it one of the most enjoyable experiences in the game.

Where do I begin...
FFVII - Basketball, Arm Wrestling, and the Fighting game (not to be confused with the Battle Arena) are pretty bland and terrible. Speed Square is also kinda crappy without a Turbo Controller...

FFIX - Tetra Master, cause its pointless, its not fun, and its totally random. Honestly the worst minigame ever imo.

FFX - All of them, especially Blitzball.

FFX-2 - The Matchmaker and PR campaigns in the Calm Lands. The Chocobo game is also terrible.

DMC Series - Special Trials, more aggravating than fun.

Persona 1 and 2 - Judgment 1999, though to be fair it only applies to any game that isn't Blackjack or Poker. Cheating bastards...

Thousand Arms - Trivia game with the last girl, she asks you stuff that the game never even tells you about (probably cause some random NPC knows it or a bad translation). Its really obnoxious.

I can probably think of more later...