That's strange, I'm always pretty sure what minutes my players get in scrimmages. You just need to choose your opponents better.
Your opponent in scrimmage shouldn't really have that big of an effect to the minute management I believe.
Are you saying it's hard to get 48 minutes in a scrimmage??? I completely disagree.
Depends what kind of minutes you want to your other players.. Because I think there are too many "quirks" in the system - with 5 players it's easy but with more players you need to assign a role to them and you should try not to blowout and so on. The system really doesn't work the way I would intuitively expect it to, and that's the (little) problem here.
You said earlier that training shouldn't be easy as people want to play challenging games. Well, that's not really an argument to either direction. Others like more challenge, others like different challenge. Now if they for example made enthusiasm hidden or game shape hidden the game would be more challengin to play well, but I guess (almost) no-one would really like that.