For whatever it is worth, here is some background. In the initial years of this game, there was only substitution by minutes and it had lots of issues.Those you report and pothers.
Fatigue was launched as an improvement and acclaimed. It was regarded by most or all users as better.
The conventional wisdom is that fatigue works better unless you need to get specific minutes to certain players - to keep promises or otherwise.
I know that I see periodic puzzling results in fatigue mode - but I dont sweat them, since I am convinced it is better than minutes approach. I do play with depth charts. I dont know any way to articulate rules that govern the tinkers, but leaving a gap in depth chart changes substitution priority. Putting a guy in more than one position stack changes usage. Setting a sub at tired changes it a bit. Usually, most seasons, over the course of games I usually can get the minutes where I want them to be.
I have now and then played around with changing depth chart radically for a game - to alter matchups and the like. Without time to experiment over several games, I find that very hard to do with any precision
That is what I do, for whatever it may be worth.