Something I have yet to see anyone else mention, probably because it's so damn vague, is the similarity between Prototype's Web Of Intrigue cut-scenes and the cult hit movie Dark City.
If you've seen Dark City, you might remember the end of the movie when Kiefer Sutherland's character injects years of memories into the main character's brain. The montage that proceeds is incredibly surreal as he hears Kiefer's voice teaching him things as he proceeds through his regular life (it's a fake memory of his past, thus more believable, blah blah movie stuff I don't need to explain.) In any case, Prototype's scenes work almost exactly the same way; the style, the noises, and the echoed voices explaining things.
It really makes the game more enjoyable, even if I am in the dark (on purpose) about wtf the story is even about.