I didn't really have an issue with the story until I finished it and then thought about it. All this shit went down because he took down the Kingpin. He put away the seemingly most criminal person in the city, only to cause:
Another greater threat, Li
Li then terrorises the city, kills Miles' father, takes up much of Spider-mans' time
Leaving little time for Peter, causing him to not be able to help Otto and preventing Doc Ock from happening
Causing a big break out at the Raft with all the biggest and baddest super villans (Can't remember if Fisk was here, if he was, then where did he go?)
Which, in turn, causes the Devil's Breath to be unleashed upon the city killing hundreds (thousands?), including Aunt May
He has to kill the one guy whom he looks up to, Otto. Basically now his third father figure to die
And the "redemption of Sable" was weak and underwritten. That turn around was way too sudden.
Moral of the story: Do the good thing and bad things will happen because of it..? He's basically a two time orphan by the end of the story, having killed his mentor, being respoinsible for his aunts (and several others) deaths, putting New York under marshall law due to enabling Li. Spider-man set these things in motion, J. Jonah Jameson wasn't wrong about that.
But when it's put like that, I just can't look back at the story and feel good about it. Please set me straight, tell me I'm wrong. I want to be wrong in this.
But other than that, I really enjoyed the game.