Minigames like those in Breath of Fire III (Pull the machine out of the sea... Pull the water out of the well...) supremely annoy me. On the other hand, some minigames are really fun. I used to have a savestate just before the on-stage battle between Zidane and Blank in FF IX because it was such fun.

Effeminate party leaders also need to go. Have you seen the protagonist in Dragoneer's Aria? I was sure it was a girl until I checked out the character's description in the official website, and I was like "w00t?!"