I think adding a more specific injury system could help.
For example, when a player gets injured, the game should specify the exact injury (broken toe, pulled hamstring, etc) and let the manager decide if he wants to play the player. A lot of NBA players still play when they get injured. Perhaps temporarily decreasing the injured players' efficiency and abilities in game would make it more realistic and give managers more control to their team, then when the player recovers, everything will go back to normal. For such injuries such as a broken arm, obviously a player wont be able to play, but a sore finger most likely won't keep a good player off the court (might negatively affect his jumpshot though ;] )