Option 3: Strictly Follow Depth Chart (SFDC):
Most of the time this will result in minutes you can understand. Starters will play 36-44 min depending on stamina. Starters will play less minutes in a blowout situation. Unfortunately the AI is not as smart and will sub out everyone at the same time usually. This option will manage 48 minutes pretty well for training purposes if needed. Another issue is that players are normally stationary so that if someone fouls out, their backup will take their place even though a different starter may be more well suited for the position.
Two things:
First, if you can get your players' stamina low enough and the backups are relatively decent, you can get starters to play even less than 36 minutes. It's sad that stamina is more of a problem than a benefit, but that's just how it is.
On the fouled-out player substitution, it's worse if you have a guy trying to go all 48 who fouls out. My experience with that is that the coach seems to pick the backup who is least needed (least likely to come in normally), rather than picking a player best suited for that position.