The tier system that was created by All-Pro Football 2K8 (2 gold players, 3 silver players, 6 bronze players) requires a lot more team building strategy than simply fielding a 99-overall super team, plus it puts every club on a level playing field, regardless of how much time or money users have invested in the mode. That is a system that could easily be implemented into all current versions of Ultimate Team, since they already split players up into "gold" "silver" and "bronze" categories.
EA's NHL series tried something similar by using salary cap restrictions for certain tournaments, but that method doesn't work well, because users will just exploit the system by filling their fourth line and backup goalie position with the lowest-rated cards in the game, which then allows them to put All-Star players on their three other lines.
All-Pro Football 2K8 provided the blueprint for how to do fantasy team modes right, but no other game has followed its lead, largely because the game makers realized that it was more profitable to just let people keep grinding away towards their 99-overall super teams instead of saying, "Here's all the players, here's your team budget, now go figure out the best way to assemble them in a realistic lineup."