If ifs were fifths we'd all be drunk.
We disagree. I think people would be really disappointed to play as a Patriots and not see Tom Brady on the team, particularly in a AAA sports game where graphics and player likenesses powered by those graphics matter a helluva lot.
IANAL and all, but with as litigious as the NFL is, I have to assume that if any unlicensed football game with NFL rosters falling out from user-generated content clawed any significant amount of market share away from Madden, the NFL and NFLPA would immediately cease-and-desist the customization functionality out of the game. They'd point to the the various player likeness court cases which took down NCAA Football as precedent, and that'd likely be the end of it.