I think that is a great idea, but I have two points. First is that a lot of teams have starters/ key players with very poor stamina. Your idea would make those players a real liability, which isn't a good thing. Second is that there shoud be a low limit as well for guys with high stamina. Say if they don't get at least 80 minutes their gameshape drops.
Overall I really like your idea. It would make stamina training a much more important factor, which would lower salaries in general, which is a good thing. I think it, or something similar, is very worthy of discussion.
Once I scored a basket that still makes me laugh.