Here is an excellent article published by the Wall Street Journal about two recent Nobel Prize winners that applied economic theory to the NFL Draft: http://blogs.wsj.com/economics/2012/10/16/a-nobel-winning-idea-to-fix-the-nfl-draft/
The writers suggest a bidding system whereby each team can bid on their most coveted draft prospects, and player goes to highest bidder. Teams are allocated different scales of rookie money based on performance during previous season. The article makes a notable point that sometimes teams draft a player that does not fit their scheme, and the players football career maybe cut short as a result. Here is an excerpt:
"Part of the problem is that there aren’t enough NFL teams for the amount of talented players trained in the college football system. Every year, each NFL team unceremoniously cuts players who have the physical and mental ability to be starters without ever giving them a real shot. Success in the NFL is almost random, and that makes it even more important to have a system in place that matches players with the right teams."