Ain't It Cool News points out that the print version of this article from the Albuquerque Journal includes a possible hint at the storyline for The Avengers. The article says:
"The Avengers" script will blend "Iron Man," "Thor" and "Captain America: The First Avenger" story lines as the Avengers battle with two alien races, the Skrulls and the Kree.
While the article features quotes from people involved with bringing the production to New Mexico, there is no confirmation that the Albuquerque Journal got this story information from Marvel Studios or Disney, so we'll have to wait and see if they are indeed going this route.
The anticipated movie is scheduled to shoot between April and September of 2011 at Albuquerque Studios, as well as in New York and Michigan.
Starring Robert Downey Jr., Chris Evans, Chris Hemsworth, Jeremy Renner, Clark Gregg, Scarlett Johansson, Samuel L. Jackson and Mark Ruffalo, the Joss Whedon-directed film opens in theaters on May 4, 2012.
UPDATE: ComingSoon.net has confirmed that the information published in the Albuquerque Journal was not officially released through Marvel Studios and can instead be attributed to a research error on the part of the newspaper.
While this does not preclude the film from featuring the Kree or the Skrull, there is no hard evidence to date to suggest their inclusion.