I'm not sure I understand all the hate for Yuffie. If it's the part where she steals the team's Materia, it's 100% skippable. You don't have to do it.

As for my most hated list, most of which were not options:
-Locke (VI): He starts the game being told by Arvis to go save Terra. He argues back, calling her a witch. Then he finally and reluctantly goes to do the rescue, at which point the Moogles come along and do all the work for him. He then spends the rest of the game creepily obsessing over protecting women that don't need it. His view that female military generals are weak and need protection doesn't make him endearing; it makes him come off delusional. He also doesn't have a single battle skill that someone else can't do better.

-Irvine (VIII): Another guy trying to get with every woman in the game. That alone is enough to put him in my top 5 most hated characters, but then they refer to him as a gunman and sharpshooter...and he freezes up when it's time to pull the trigger. By this point, he's already #1 most hated for me. But then he watches Rinoa fall off the edge of the garden, is unable to do anything. He then tells Squall to go rescue her...IN THE MIDDLE OF LEADING A MAJOR FIGHT BETWEEN GARDENS. Not now, Irvine. You do it. And then there's the orphanage scene. It's long, it's boring, but every time I try to leave, Irvine won't let me. C'mon Irvine, I've seen the scenes before. Can I just get on with the game?

-Auron (X): When you're in a game with Tidus and Lulu (not to mention the moment where Yuna gathers everyone out into a thunderstorm to deliver news she could have said inside) and you're worse than both of them, you must really suck. And Auron does. He's a know-it-all, he's bossy. He acts like he's running the show and doesn't care what Yuna does, as long as she continues the pilgrimage for him. Meanwhile, he's near useless in battle later in the game because he's way, WAY too slow. One battle forced him into the party and it took about 4 turns from everyone else before he got one so I could switch him out.

-Vaan (XII): He's really not that awful, but being forced to play as him in cities with no option to switch makes me not like him.

-Snow (XIII): XIII's version of Auron: the guy who thinks he's better than everyone else. Add in the endless yapping about being a hero, and there we have a character that grates on the nerves.