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Where to start, you ask...**cracks fingers**
First, I would start by ensuring your minor league coaches are not duds. I'm assuming you have minor league personnel contracts set to the AI. The AI is very bad at hiring coaches in my opinion. Take control of that and sign the best you can find.
Second, take control of minor league promotions. Demote players that are batting below 90 OPS+ or pitching with a FIP- higher than 110. Promote players batting above 120 OPS+, or have a FIP- lower than 80. (Note this is just for the initial run of re-organizing your minors).
If I'm trying to minimize the amount of time I spend controlling minors, only check halfway through the season to see if someone deserves an early promotion. Otherwise, you can leave promotions alone throughout the season, provided you have adequate backups at all your levels.
Next, treat your AAA and AA teams as ML reserve teams. You want to prioritize winning at those levels. That means sign ML free agents on minor league contracts. Good personalities are a nice bonus. Your prospects that are good enough to play at those levels will benefit from the ML experience and positive role models around them.
Do this, and your minor league teams will win more, thus improving morale which will in turn aid prospect development. I have a more comprehensive guide in my signature block, but it's a few versions old at this point.
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