I am not sure that Walt ever had that much of a soul. I think that he was just beaten down when the show started. He had gotten wrapped up in a life that he hated, and was just pushing through it. His choices have always been pretty selfish, and ego driven.
For me the thing that makes the show work so well is that Walt is a genius. He is not just some middle-aged chemistry teacher. Because he is a genius it is believable when he works things out, and doesn't get killed in the process. I don't think that being a genius makes you less moral, but I do think that it makes you less beholden to the ideas of right and wrong that most of us live under. But then again "Just because you killed Jesse James, don't make you Jesse James." So maybe Walt is a good guy caught up in a whirlwind, but I doubt it.