Getting back to whether or not the movies leading to this was Earth 616 or Ultimates, I have an article here in a local paper that say that the current president of MarvelEntertainment, Kevin Feige, was having issues with how to have it presented, until he hit on Bryan Hitch's rendition of Nick Fury. The Black Nick Fury, and how the Ultimates brought a more modern edge to the series.
There also a lot of things from this movie that scream Ultimates. Hawkeye was not one of the original members of the team (not to mention his costume is an almost direct lift from Ultimates.) Black Widow also wasn't a member of the team from the start. Nor was she a S.H.I.E.L.D. Agent at the time they formed in 616. She was in the Ultimates universe. The aliens not being Skrulls, but Chituri (?), also from Ultimates.
There's enough evidence to me that pretty much says it's mostly Ultimates, but luckily took enough from 616 to make watching the movies palatable. For which I am incredibly thankful, cuz yeah, Ultimates sucked I terms of characters.