Tidus. Not so much for the fact that he whined as for the fact that he's pretty much as dumb as a rock. I tried to count how many questions he asked that I had already discerned the answer to, but lost count about halfway through the game. I think I'd gotten to about thirty.
Beyond that, Cait Sith kind of annoyed me, mostly because he was so easily replaced once we thought we were rid of him, and Wakka's fanaticism and racism got on my nerves at points (although not as much as they would've if John DiMaggio hadn't been his voice actor). Wakka's character arc was somewhat more redemptive than Tidus's, though, I felt, because Tidus never really stopped asking pointless questions.
Rosa also annoyed me, mostly because she was pretty much the walking embodiment of everything feminists hate about traditional fantasy literature. Also the fact that some versions of the story in Japan evidently have her leaving Cain for Cecil when Cecil became more powerful, though I've never been able to get a direct translation of the part of FFIV's Ultimania equivalent that contains this and I would've expected it to have been in FFIV DS. Even if that turns out to be incorrect though, she still annoys me.
Also, pretty much all FFX-2 editions of characters. There are other characters I would consider 'overrated' but not 'least favourites', but cba listing them.