I liked Shadow the hedgehog (The character, not the game): He's got an interesting personality, moral code, along with solid backstory and character development (In that he actually HAS backstory and character development). I also have a bit of a soft spot for Snow Villiers, namely because i just like his character design and the fact he can summon up a FUCKING MOTORCYCLE!
While not necesarily hated to the extent of some of the other characters, Caim from Drakengard isn't necessarily well liked either. Some call him a bit one-dimensional/Under-developed or just downright too fucking evil to be a protagonist...but that's why he's so fucking perfect! In a genre where characters like Tidus are pretty much the norm for lead characters, along with the downright whiny protagonists...to get a character who didn't give two shits about the world that was falling apart around him or his allies, and who's only goal was to murder every single enemy in his way with a smile on his face was rather refreshing. In an odd way, Caim was just so unlikeable that he was likeable (If that makes any sense).