Here's the thing though.. while the NFL doesn't own the teams and doesn't reserve the rights to sign them over exclusively anymore, that doesn't mean they lost any control over the player's association.
There have been games in history to have the player association licence and not have the NFL licence (
http://en.wikipedia.org/wiki/Madden_Football_64 ), but I haven't seen a game with the NFL licence and no players licence... though I wouldn't be suprised if there are some out there.
"On December 13, 2004, EA Sports announced it had secured exclusive rights to the NFL and its players' union for the subsequent five years, precluding any other third party from selling a football game using NFL players, teams, stadiums or other licenses. This was recently extended until 2012."
http://en.wikipedia.org/wiki/Madden_NFL
That implies that Madden DID in fact get the player association licence exclusively. If they didn't, Sega probably would have been releasing football games just like Madden 64/93 in the down-time. The best Sega could do now is get all of the teams to agree to be on their game, and they can make it like a college football game with no real player names.
I really don't think people are that desperate these days for a 2k game.