I don't think it's THAT doom and gloom.
MiLB is shrinking but only by something like one affiliate per organization, at this point. Baseball is the type of sport that takes years to develop in. There isn't a chance the general structure of MiLB will change in any drastic way; there should at least be AAA/AA, A ball, short season, and rookie ball. Organizations need different levels and multiple affiliates for various systemic reasons.
What has become obvious over the last few years is that MLB organizations and MLB generally are not capable or willing to provide adequate resources and compensation to all participants in their MiLB system. You can argue that it's actually ETHICAL to employ less MiLB players.
If long-shot prospects want to pursue their MLB dreams, there has never been a better time to do that through Independent baseball leagues. This was true before the contraction of MiLB and it was based on technological advancements. Team can "scout" data-based factors like exit velocity, spin rate, pitch velocity no matter where a player is playing. We have seen players get signed from viral tweets of their bullpen sessions.