"The new proposed system will provide MILB players with far better and more consistent instruction (which leads to more rapid improvement), better facilities, access to better athletic trainers, better nutrition, etc."
Not sure I understand the comment. Better facilities are not suddenly going to appear for those teams that survive this weeding out. Yes, the bad franchises with bad stadiums will go bye-bye, but the survivors are then set with what they have already. And the top levels of the minors already have the focus on instruction, nutrition, etc. Why will eliminating low A and Rookie ball change that?
What will also happen is MLB will continue to lose fans, the ones in the small towns who came out to see Mike Trout when he first started and now follow him with the Angels. Those towns that no longer have MLB affiliations will lose interest in the sport--just as St.Louis and San Diego have less NFL fans now than they did three years ago. Over time that becomes significant. Maybe MLB doesn't care since small town fans are not producing much revenue in ticket sales, but they do watch TV and the playoffs and World Series.
Summer night baseball in these towns is affordable entertainment for most of the residents who will no longer have that or any connection with any particular MLB franchise. They are gone as baseball fans, but maybe MLB has done the math and said good riddance.