The ability to set off-season (or spring training or fall league) programs for players. Let me give a few examples:
"Tell Batter to Bulk Up": He gains a random number of points of power. He loses a similar number of points of range and speed.
"Move Starter to Pen": He gains a number of points in velocity and maybe splits. He drops Pitches 3-5 but maybe the rating of P1 and P2 goes up. His stamina plunges. Basically you turn a 200 IP guy into a 60 IP guy.
"Concentrate on Fielding": He gains at a faster than expected rate in fielding categories but suffers dramatically at the plate. Maybe you want to turn him into a no-hit, all-glove utility infielder.
The rating changes should be a net minus across all players. While some guys might have positive overall results, the sum of total of players should get worse. Some batters lose 10 points of speed but don't get gain any power. Some relievers lose stamina but don't get any better.
The size of the change in values could be based on age and body type and makeup. For some players (maybe those with room to "fill out" based on their height and weight) and those players that are young, the swing in numbers could be higher. Also, players getting better coaching and with more success in the minors could be more likely to see larger or positive improvements also. In other words, a 26 year old minor leaguer that is 5' 11" and 205 pounds with bad coaches in a dismal farm system just gets fat when you tell him to "bulk up".
Another benefit of this is that there might now be some value to drafting marginal major leaguers. Maybe it is a guy you think you can turn into a valuable role player. Maybe it is guy you think is "projectable" because he is 6'2" and only 175 pounds.