Right now when a player is in foul trouble at any point in the game (i.e., 2 fouls in the first minute is also a problem), it makes them weaker defensively, and the effect is increased substantially for their 5th foul.
In addition, your coach will tend to sit a player in foul trouble, but it's not quite an ironclad rule. Rather, what happens is that the coach considers him a bad option, but if he's better by enough of a margin over his replacements, then he will continue to play.
I think the penalty may be too severe, and need tuning. Right now it's like a player is put in leg irons if he has 3 fouls before 6 minutes in 3Q, and then these are unlocked at that time. The GE sees that a player is in leg irons, and unless we are comparing stupendous in leg irons with an atrocious sub, the starter sits.
I don't think there should be much effect, if any, if the player is below the average fouling rate that would cause him to foul out (8 minutes per foul) that there should be any penalty.
So if there are ML minutes left, and a player has FTG fouls to give, where FTG = 6 - PF, and there is an effectiveness coefficient of EC. Then the FT effect would be
EC * ( ML/8 - FTG)
If this is negative, there would be no penalty. Let's say that EC were 20%.
Then a player with 1 PF would be fully effective from about 8:00 remaining in the 1Q. A player with 2 PF would be OK from 8:00 left in 2Q; 3 PF from half time; 4 PF from 4:00 left in the 4Q; and 5 PF from 8:00 left in 4Q.
But even before those times, the penalty would be small enough that a starter could usually stay in the game with one more foul, unless the sub is of comparable ability. This would add the risk of a player getting another foul. But currently, it appears that the penalty is geared too much towards making sure that a player almost never fouls out, except in desperation time at the end of the game.