Oh boy, that's a toughie. Because I hate quite a few characters.
First, from Final Fantasy 4, there is Edge the Ninja. Now, usually his high attack and elemental Blitz moves are very useful for getting through random encounters. Bosses however are a different story. You see, Edge is supposed to be the fast and hard hitting one, but the upshot is that he has low HP and very little defense. In boss fights, especially towards the end, he manages to die so often that it's not even worth reviving him. You end up being left with the option of either putting him in the front row to do some extra damage at the start of the fight, or putting him in back and compromise his damage dealing ability but gain a slim chance that he'll survive more than 3 turns. Also, towards the end when every one has the best equipment, Kain and Cecil STILL do more physical damage than he does. So bravo for making random encounters slightly easier to deal with, yet being utterly fucking useless when some extra fast attack power would actually needed.
And then Navi. Hey, YOU listen Navi...shut up.
And Miranda from ME2...god dammit, I hate her so, SO much. It's like, she exists for no other purpose than to try so very hard yet fail miserably to add some kind of sex appeal to the game. Every dialogue scene with her is either focused on her butt or her chest, her voice is just a dull monotone and she has absolutely nothing interesting to say. "Oh, my daddy made me sad so I ran away from a life of luxury 'cuz I secretly have a bad girl side".
And EVERY SINGLE CHARACTER IN METROID OTHER M. Adam Malkovich was built up in Fusion to be like this awesome, brave, super-intelligent war general sort of guy. Now he looks like a Final Fantasy reject in a generic sci-fi space suit who stops just short of telling Samus to make him a sandwich. And then of course there is Samus herself, who would not just make him a sandwich but apparently would happily burn to death while doing so. But really that was just a case of them being poorly handled. They were bad characters in that particular story, not always.
Uggh, that's my ranting for the night.