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Yes, according to Joe's interview with Hitflix,“We will see the Captain America villain, the main villain, the Red Skull. But it's the origin story. It's how he became Captain America in World War II. There are present-day bookends, but it's really... it's his origin story. And we decided you only get one shot at telling an origin story, so you might as well tell it first."
The director is also not that worried about the pressure to blend his story with the planned Avengers team-up Marvel has set for the future. “It's like any other project. You read the script, you decide how you're going to do it, tell the best possible story. Then they'll take The First Avenger story and incorporate it into the bigger franchise, you know? I'm not worried about that. We have a great story and a great script, and we have the resources to do it right. I think it's going to be a lot of fun. We're shooting in the UK because most of the story takes place in Europe. We're casting now, and then we start shooting in June.”
So, the question now - who is Captain America?