If you look deep enough into the decision USSF made to create the Academy program you will likely find Nike influence as they are the sponsor of the National Team. On the other side of the coin Adidas has their ESP program.
Given the fact that Academy players aren't allowed to play anywhere other than in the Academy and for their High School, I for one seriuosly doubt Adidas will quitely give up on having access to some of the top players in the country. How will they handle it? The two companies will influence clubs within the Premier League and the Academy in an effort to build programs designed to attract top talent their way.
Make no mistake, both of these companies are involved in what appears to be a new divide of Elite soccer in the US.
I don't think we'll see local retailers involved from a branding standpoint. What you'll see is a fight for control of access to players through clubs participating in specific leagues. Ultimately, the winner will be the players as companies compete for their business.
Reference this link for the Adidas program:
http://www.adidas-esp.com/Home/Index.asp