Is there already an option for this? If not, I think something like this should be available. Also, to expand on the idea other stuff like the option to have your players with better defense in the game when your team is winning late would be nice.
I think the coaching AI is such that if you select "Let coach decide" or "Depth Chart until 4th" for your substitution options, the coach tries to put out the lineup that has the best chance of winning the game for you at the start of the 4th quarter. Then again, in my experience, it's been my starting lineup, so I don't know if the coach is really smart enough to know who the best position players are or if he just goes with the starters you selected.
I had suggested something similar here
(145161.1). Not exactly what you're suggesting, but along the same lines. Basically, more freedom to decide what coaching decisions are made during the game instead of just one instruction at the start of the game.