That's a problem, but not the problem.
If my awful stamina SF is backed up by a much worse player, he subs out without fail. If my strong stamina PG is backed up by a similarly bad player, he doesn't come out of the game. So the problem is directly related to stamina.
As far as quality players go, there are sound strategies in which you use bad players to eat minutes in easy league games, to save salary. If an owner sets his sim for "strictly follow depth chart," the coach should follow that depth chart. It's absurd that a player with strong stamina becomes some sort of renegade who can successfully tune out his coach, just because his owner had the nerve to make his stamina better.