Before I start my complaint/suggestion, I'll say that yes, I know that there is some benefit to fielding a competitive minor league team because your actual prospects might get an extra development cycle in the playoffs.
That being said, the vast majority of a team's minors consists of largely interchangeable trash that will never sniff an ML roster. I (and I imagine many) don't really care how much of what position they play. It would be nice to just let the simmy run them.
But there's a problem, you have your handful of super important actual prospects. If you don't micromanage your minors, the sim is liable to have them languish on the inactive list.
So, it would be nice to have a "maximize playing time" button for your true prospects. That way you can set your minors to auto-pilot, and the sim knows that these guys should always play if they're above the rest cutoff, and they should always be the first pitcher used if they're rested.