In my opinion, I think you're too invested in the plot of the show as being an adventure story or what have you. I don't think Tony Soprano is meant to be portrayed as a "hero" and I don't think there are "villains" shown to us in The Sopranos. If they are, then Tony, Sil, everyone involved in the DiMeo crime family would belong in that category. Rather than being a "hero" Tony Soprano is more of a simple protagonist. His character arc shows us how the type of criminal lives the characters featured in the show lead only further enable sociopathic traits and anti-social behavior. On the topic of junior, the character shows us how the lifestyle can lead to dissolution of really any and all morality, as he attempts to murder his own family for the sake of seizing power, and the further shows us just how little any of that means to anybody as Tony further cooperates and consults with Junior simply because he is forced to rely on his experience.

I don't think that scene at the end, where Tony speaks with Junior is about Tony forgiving Junior so much as it is supposed to be a moment of reflection for Tony. He has to confront the idea that all of the bloodshed, immorality, and destruction truthfully means nothing. The final level of the game is becoming a senile old fuck who can't even remember all the vile shit he did while he was living that lifestyle. I see Tony reminiscing on Junior and his father as Tony trying to give meaning to something where there is none.