I've thought of a few creative fixes to the coaching problem:
1. Have minor league coordinators. Similar to how there's only one fielding coach, make there be one minor league coordinator for hitting, fielding, etc. No individual coaches*.
2. Set a budget for each level on how much you want to spend (ie. 250k AAA, 75k rookie, etc.). You wouldn't actually hire anybody, you would purely just say "I want to spend 250K on AAA coaching)", etc. You'd have a minimum for each level, but you could just invest however much you want over that into each. Maybe this can be done after major league hiring, so people can utilize 100% of their remaining budget on the minors. This would also mean no individual coaches*.
*Obviously if there's no minor league coaches, then how would they develop into major league coaches? I would suggest 1 of 2 solutions:
1. New coaches are produced each year similar to rookie ball, except they start with ratings in the 70's.
2. Have the system "assign" coaches based on your level of minor league coordinator or budget invested. These coaches would develop as they normally do.