A two tier system is absolutely necessary, because in real life there's a big difference in sustaining effort in a short span of time and the effects of a long time effort.
NBA 2K, as some said, implemented this years ago and it works brilliantly:
- Short-term stamina bar depletes while you sprint but recover when you rest, so you can't just sprint all over like a headless chicken.
- Long-term stamina depletes gradually depending on the efforts and the stamina of the player.
This is an absolute must in football games and the reason why intelligence and strategy play such a small part in the game as it is now, both online and offline.
I guess the reason why they don't put it in is due to the ammount of work they should do to balance things right (and probably they would continue to cheat in single player to balance the AI). And they are too busy fixing other things and adding untucked shirts and different hairstyles.
Though it's just the kind of thing you would expect developed by a company whose moto is "the pitch is ours", right?