I think Sega/VC's only shot now would be to put out a football game similar to what NFL2K6 would have been, just without the actual team names/logos/players. So you still have the same cities, conferecnes/divisions, color schemes, player numbers, maybe player initials instead of names.
But the real way they could do something would be to combine this with an extreme amount of online and customization options. First of all, make it real easy to patch the game to include actual teams/logos/players (done by a :cough: 3rd party of course). Then allow for a much better online system than Madden has. Allow people to create their own teams, join official online leagues, etc... really put the online aspects above anything else. If the gameplay is good enough and online play is top notch, I think people would be willing to look past the lack of NFL/ESPN logos everywhere, especially if the game is $19.99. A lot of people played games back in the day without NFL licenses (madden pre-NFL, Tecmo, etc...).
Still the loss of the licenses is going to hurt and even if they could come out with a game like I described, they might feel that the sales just wouldn't be high enough to justify the effort.