How many times have you played with a character you hate? I am not meaning a character who are weak or have a weird design. I am talking about a character that you despise his/her/its actions. A character that made you want to stop playing because he is an asshole and you don't want to do what the character do. Games have very little characters that way.
Kratos is possible the most well known. There is nothing to like about him. He is a mass murderer sociopath, who will kill anyone (and anything), that dare to cross his path. Or just kill people to accomplish his objectives, no matter what. In God of War III, he kills Poseidon lovers to solve a puzzle. She was not doing anything to stop him. She was just there. And yet Kratos took her and throw her inside a door's gears to keep it open, killing her. He also killed Hera, Zeus' wife, just because she got in his nerves.
He did this to get his revenge against the gods. There is no noble objective here. It is not to save mankind or to rescue a beloved one. He is not being under mind control or being deceived. He did this awful acts because he is an evil character. There is moments in GOW3 that hint he still have some compassion left, but most of the time he is just a merciless killer.
Most games don't give you a detestable character like Kratos. Most justify evil acts done by the character the player controls as either justifiable or beyond the character powers to avoid. It make sense, from a business stand point. Nobody want to be the bad guy. Even when playing with an anti-hero we want him to be a badass with noble heart.
Kratos is not that. He is badass, but far from noble. He is the first (and till now) the only character I have played that made me question keeping going. I will never like him as a hero. To me, he will always be one of the villains in the GOW series. And I think this is a great thing.
Feeling remorse because of something you done in a game is a good thing. Regretting not being able to save a good character or being directly responsible by its death is a good thing. It is all fictional, but it is always good that something make you reflect what just happened.
I think more games must do this, letting the player experience the 'dark side'. If done correctly, it is a powerful tool to lead to reflection.