In the 1920s the International League Orioles were probably among the top 10 professional teams in the world. Jack Dunn refused to sign affiliation agreements. He had all stars and Hall of Fame caliber players in their prime. But eventually he was pressured by the rest of the league into caving. The PCL made a little run in the 1950s at going independent and hinting a going major, but expansion and the Dodgers and Giants put an end to that. Besides the relatively low-level indy leagues today there haven't been real minor league pennant races in my lifetime.
It's premature to say that the MLB draft is moving to August. MLB wants to move it after the College World Series. Some have speculated that August makes sense as a date in August would eliminate the need for short-season A teams.
Logically, it makes no sense to mandate which minor league teams will be axed although "leaking" a list may encourage towns on the fence to up their facilities. How up to date are the facilities in Frederick? It location is great.
Organizations such as the Orioles/Astros that are big on machine learning, regression models, and neural networks are more likely to be on board with this plan while organizations such as the Cubs/Yankees that have the resources to have a more balanced approach may have misgivings. During the past season the Cubs had 300 players under control. This new plan would lessen that number by at least 100.
Youngsters that are unable to make the jump from the DSL or HS to full-season ball may stay at their respective complexes and play unofficial games against other organizations throughout the summer as opposed to until the draft as in past years.
One advantage is that it will be easier to evaluate prospects with fewer non-prospects in the mix, although you could argue that 20-year old prospects benefit from playing with 25-year old non-prospects who know the little things but have limited tools.
The great statistics put up by top prospects during their first ML seasons in recent years suggests that top prospects may be spending too much time in the minors. More rapid promotion for a select few is likely with a thinner pool of players.
It is also possible that AAA will be more like AA is today, i.e., the place for top prospects. Independent leagues comprised of released players could fill the role that AAA has today - although this will depend on the details of the next ML agreement.
I've also heard that some teams would prefer a shorter season so that their prospects could spend more time in their respective pitching/hitting labs.
I think their short-term plan would be to just have complex type leagues in Florida. Use the spring training sites. Intersquad games, eventually set up schedules to play other teams. And release all the random organizational guys.
MLB has all the leverage here because a large number of MiLB teams need MLB money to exist, and the majors don't really need the minors. MLB would be largely unchanged if the minors disappeared tomorrow and was replaced by all the real prospects just hanging out in Florida and working out, playing scrimmages.
But... maybe way back in the MLB owners heads is the idea that if they totally dumped bigger minor league cities new, bigger, more powerful independent leagues could spring up. Players who don't like their draft position or bonus could have an alternate place to go, at least for a while. I don't know if a 3rd major (really 2nd since AL and NL are just one league) is even marginally viable, but a fully independent AAA-ish league could seriously annoy the majors.