Okay I know I am in the minority about this, but I'll throw it out there anyway. I do not like the idea, from a game playing point of view, of allowing man defense to set defensive match ups. I prefer forcing the coaches to do research to see if the opposition changes their lineup or keeps it the same. I think if this was allowed in the game it would make man defense way to strong a defense in comparison to the others.
Playing devils advocate for a second, you want the sim to be more realistic and intuitive that y don't want your player playing that many straight minutes or to that level of fatigue because it doesn't fit your needs or wants, but want if that is exactly what I want it to do. You may calling it gaming the system, but it's really not. It's figuring out how the sim works and making decisions with that information that makes the sim run your team the way you want it to. When you give up trying to force your thoughts of how it should work and learn to work the engine you'll discover you can get the engine to do exactly what you want it to do and then you I'll have an even better advantage of the other less intelligent coaches in this game.
Seriously, set it to fatigue and accept the help to get the engine to run the team the way you want. You're not wrong in your assumptions about the sim or how it should work you're just not using the right commands. There are plenty of good coaches still willing to help you learn the engine for what it is not what you want it to be