Shinji is the most human character I've seen developed for an anime, he's a major depressed, socially phobic, emotionally stunted, terrified little boy, with major abandonment issues and an oedipus complex. In spite of the fact that he's about as messed up emotionally as you can get short of suicidal, he's all but forced into being saviour of the whole damn world.
Shinn Asuka was severly truamatized, possibly explaining most of his actions, however, Gundam Seed Destiny wasn't particularly interested in developing real characters and giving them depth, thus he comes off as a one dimensional anti-hero who can't see anything that's going on around him, much less come to any realizations.
My most disliked character is Naruto, I'm afraid my hatred of him grew considerably as the filler went on. I think what bothers me most about him, aside from his annoying personality, grating voice actor, dumb catchphrase, and endless redundant thematic points, is that they never force him to kill anyone. Everyone else at some point seems to kill someone, they remove him from taking lives because he's a protagonist, it annoys me to no end.