I only leave AUTO training on for low level minor league guys that need work in all areas. For anyone else, I manually set training on areas they need work the most. For example, I started a test Diamondback's franchise. Auto training had Yasmany Thomas set to baserunning drills. Well he is like a 50 speed and Stealing was only at 10 or something, so why bother with this?? Just an example of how Auto training wastes effort in many cases.
Generally I set training on important areas and leave it for a couple months at a time. Or switch back and forth between a couple key skill sets every other month. So basically I'm focusing a player's training on just 2-3 skill sets per season. Age and Potential will factor in to their progression or regression in all areas. If a young minor league player with a lot of potential gains 2-3 points in all categories just due to normal progression, he may see 5-6 points in the areas you trained him in manually, if you focus on just a couple areas for the whole season. Likewise, if an older player starts to regress by a couple points in all categories naturally, if you focus his training on a couple skill sets, he may stay stable or even gain a point.
Just my experience, other folks will probably advise differently.