Hm, Patrick, you bring up a truly intriguing point on our perceptions of characters in stories, especially in video games, (where we have the ability to literally play out the story) where our interactions have an impact on the world but not the plot. A rogue-like, Han Solo esque character that comes to mind for me is John Marston and is a great foil to Aiden's, seemingly, non redeeming qualities and actions.
In Red Dead Redemption, the game in which Marston is the key figure, we also have an impact on our environment; much like in Watch Dogs. However, unlike in Watch Dogs, Marston's plot line takes a much more liberating path that has the player, and the character, reach an incredibly cathartic moment by the end. And, Red Dead's ending almost acts as a foil to Watch Dog's; pulling any sense of control from the player, and Marston, putting you before the void and telling you to dive in without any other choice.
Marston's history is rather similar to Aiden's, in regard to their sordid pasts. However, once again we have Marston truly trying to atone for the dark deeds of his past while continuing to commit atrocities more on the level of a mass murder; much like Aiden. Unlike Aiden, however, we have a true sentimental connection to Marston and feel that what he is doing is truly building a bridge to a better future for himself; whether it's by liberating a small desert town from an unruly gang or overthrowing a harsh, despotic, Mexican dictator. Simply, Red Dead Redemption built a fairly basic connection to his family, his land, and his desire to live a life in peace -something most of us wish for at some point. However, this plot device serves a much better basis for building an anti-hero that doesn't feel as though he deserves his ill begotten fate, despite his truly deplorable actions and past choices; most of which were circumstantial.
This is an interesting topic that really does deserve the attention of game developers. As creators, game developers deserve to give their characters a sense of life and awareness. Clearly, Aiden is not aware that he has created his own awful fate, and whether the developers knew this or not is in their ball park. However, as consumers, We have the right to say that their portrayal of this character type is not realistic or not emotionally significant, and/or left an incredibly awful taste in our mouths.
Hopefully, both consumer and developer continue to take a better look at what we are doing with our in-game characters and how the plot line impacts our perception of those characters and our choices.