Part and parcel with the flashback assumption was the sensible conclusion that Atwell would be back as Carter, if only briefly. Atwell indirectly supported that conclusion by playing reasonably coy in answer to questions about her involvement, giving the standard I-can't-say-anything-about-that-which-means-I'm-probably-in-the-movie maneuver.
Now, though, Atwell has cut through the coyness and let it be known that she's not in Captain America: The Winter Soldier. In a TimeOut interview promoting the BBC1 series Restless, Atwell confirmed that she isn't involved in the continuing adventures of the most patriotic Avenger. That's a bummer, since Atwell's Carter was a distinctly strong character who never needed her would-be boyfriend to bail her out of trouble.
A deleted sequence from Joss Whedon's The Avengers revealed that Carter is still alive and kicking in 2012. Hopefully The Winter Soldier will continue to explore Cap's discomfort as a man out of time, and the sequel could dive into that by having Steve pay a visit to an aged Peggy, perhaps played by an age-appropriate actress.
A new female lead will join the party in the sequel, with a number of gorgeous brunettes having been bandied about over the last few months, though Marvel has yet to make any official announcement on that score.
Chris Evans will still have plenty of company, however. Anthony Mackie is joining the cinematic Marvel universe as the Falcon, along with Frank Grillo as Crossbones. The Winter Soldier is set to be the most SHIELD-intensive movie of Phase Two. Samuel L. Jackson, Scarlett Johansson, and Cobie Smulders are all set to return to their Avengers roles for incoming directors Anthony Russo and Joe Russo. Oh, and Sebastian Stan is pretty much guaranteed to be back as Bucky Barnes, the Winter Soldier himself.
Production on Captain America: The Winter Soldier begins production this spring for an April 4, 2014 theatrical debut.