There was no flow between the Doc Ock, Black Cat/Shocker, Mysterio and Rhino story lines. It was like they were just thrown in there because they realized, "Oh ****. The Dock Ock storyline alone isn't going to be enough to make the game last."
I wouldn't say thrown, I'd say placed, and they
were placed in there because they realized "Oh ****. The Doc Ock storyline alone isn't going to be enough to make the game last." And it wouldn't, and it isn't a bad thing either. After halfway through the game, Octavius finally becomes Ock, then they have to follow the battles and events of the movie as much as possible. Only halfway through the game we finally meet the main villain.
Mysterio, Rhino, Shocker and Black Cat were more like filler, but they were necessary to the game and only added to the story. Besides making them only side stories plot, they contributed to the overall narrative. They even bothered to make Spidey learn through different challenges, since they couldn't incorporate the "
Spider-Man No More" of the movie (where Peter loses his powers) for gameplay issues. They even bothered to present Quentin Beck and build an origin for Mysterio. They bothered to explain how Shocker escaped from prison, instead of just throwing him there once again for us to battle. They made Black Cat extremely relevant to the plot. The only downside was how they forgot about Rhino after he was defeated, but all of this shows they cared a great deal for the story and its themes, which is one of the reasons I like this game more than all the other Spidey games.
They placed each villain in the story strategically so one's presence and plot wouldn't overshadow the other one and it made the story progress through them. Not progress only in terms of time, but storywise, like having Spidey dealing with day to day threats like thugs and ocasionaly someone like Rhino, as a public figure in Beck's game and having his social status in jeopardy because of Mysterio and JJ, or growing his partnership and affection for Cat through Shocker, or acting irresponsibly because of Black Cat while questioning himself about his powers, his balance in life, his social status and what to do with it, while tying it all up with characters from the movie, like MJ and Harry, not forgeting how absent Peter was being for both but trying so hard to be present. And we can feel it all through everyone's actions and lines. You can check some of this moments that contributes to the characters development here, at 4:20 and 9:42:
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or here, with one of those inner monologue moments at the beginning, and his conclusion at 2:34:
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All of this is why the story wasn't incoherent. It followed a narrative line because everything happened at the right time and was carefully done so it wouldn't seem rushed and forced. It flowed naturally, instead of having things tossed there for us to have fun with. It doesn't need to have the main villain tied with all the others to have a coherent plot, the same way that it doesn't need to be related with common thugs or the lessons Spidey learn with other villains, it needs to be done and executed well.
Sorry for the long post, but I only have commends about the game's story. I can keep talking about other things that added to the overall presentation, like having chapters within the game with a title related to what would go on next, but it'd make for a even longer post. I can understand other complaints about the game. Some of which are my own, but the story being incoherent and not having a flow is not one of them. The game and its story had a heart, had a soul. It didn't feel shallow. The characters really felt like characters in a intrigue instead of just being polygonal figures and, even though the story is not often one of the main points when someone praises the game, I'm sure it was one of the reasons that contributed for the game being so adored.