A few of my choices have been listeded. Yay.
But I think my top-pick of hated protagonist is Asbel Lhant from Tales of Graces. (Actually, I hate just about everyone but the brother.) Anywho, this guy is just... useless. And incompetent. Plus just god damn annoying...
Well, maybe Trevor kinda beats him. Because this guy comes into the game supposed to be some kind of wild card crazy dude and never does anything throughout the entire game. Well, actually his introduction stops the games short time that Franklin and Michael had doing jobs for reasons and just kills it. Kills it. You think he'd like kill a FBI guy and then shenanigans ensue but nope. Not even. Just a waste of time, and the few times his character does shine, he's not even the same guy the rest of the game tries to portray him as.
A few runner ups are:
Kratos: No, dude, you are in no way a good thing in the slightest. The ending to your games makes no sense and one was the only good one, narratively.
Connor: Uh. He's dumb, quite so, and walks away a few times from situations either through making the stupidest choices. (There's no way you could have simply subdued your friend. Oh no. He's more skilled and athletic combatant.) And somehow your in better shape then your father, the better and more skilled assassin, after being pretty much hit by a cannonball. Not to mention he quickly, and I mean almost immediately abandons the kick out the door of working for his people.
Ezio: Simply was around too long. He couldn't support his second two games.
Everyone in call of duty Ghosts, except the two supporting Ghosts.
Master Chief: You're a god of war now and you're never going away. Your character was spent after 2 games and since 3 you've only been a drag on the lore.
Jack: Mass Effect. Oh, you're a super biotic who once took down a space station and can rip through 4 giant mechs with no problem? Hah, no, don't lie to me. She's a immature brat who wallows in pity and doesn't even back up the supposed ability she has. Not even in a cutscene.
Nathan Drake: You're just smug, not funny, and even being shot and left in sub-zero temperatures cannot kill you, even dealing with climbing up a train. I also just don't like you. You also have some pretty dumb detours and puzzles.
Special Mention: Kirito from SAO. Why? Been said already a few times.
Gah I hate too many characters D: