The NFL wants it. The NFL has easier control on what happens in one game in comparison to multiple games and the NFL can (and has) advertise Madden as the official game of the NFL in similar fashion to other products.
Call me crazy, but I think NFL Blitz played a role in the NFL wanting one game. NFL told Midway to tone down Blitz to make it a more clean representation of the sport and the league ("NFL Blitz Pro"). A year after that was when the exclusive license with EA happened.