It could even be said the movie was basically a version of EMH.I thought EMH was already skewed pretty damn close to the movies as it was... Hell the first season finale was basically a version of the Avengers movie...
But along with the redubbing of Josh Keaton's voice work as Spidey with that of Drake Bell's in EMH, this really just reeks of a decision to tie all of the Marvel cartoons into one very cohesive universe, perhaps even to the extent of using the same kind of animation and character designs currently being used by Ultimate Spider-man (we could see the exact same versions of Nick Fury and other characters in both). The upcoming Hulk: Agents of S.M.A.S.H. will probably do the same thing, IMO.