I've been trying to think of a way to make this work better, and I think I have an idea. And no, scrap it altogether isn't what I had in mind.
First off it should run strict until the halfway mark of each leagues respective season. Over the ASB, the coaches evaluate all the pitchers, determine who based on performance is likely to end up as a MLB starter or reliever then in the second half SLOWLY increase the starter's number of pitches. Just stretch him out a little. After the AS Break, The starters would no longer pitch in relief, just normal side sessions. Each league will have strict pitch counts in the first half, with the second half slowly increased to the next level's pitch count by the end of the season.
This will acclimate the SP to the next level (ex. High A to AA) while not increasing the workload to quickly. This should run from Rookie to High A with AA having a cap on starters of 90-100 pitches, and AAA should be evaluated on a pitcher by pitcher basis as it is often staffed with older pitchers an rehab assignments.
This will benefit the relievers too. Guys that lack that third pitch and are likely not going to get it won't waste development time trying to develop into something they aren't. There is nothing wrong with spending 3-4 years developing top notch reliever.