The storyline doesn't actually bothers me, and it doesn't indicates that it's not going to be addressed in the films.
In the press release, they say that it is a sequel of TASM 1: The Videogame, not TASM 1 (the movie), and that they're creating their own alternate universe, loosely based on the movies. So, Manhattan will remember the chaos from the cross-species incident, Spidey already met Rhino, Black Cat, etc...
So, it's okay if Spidey catches Uncle Ben's killer here, it'll eventually happen in the movies.