The story was leaked on Friday that Major League Baseball is exploring reorganizing and realigning the minor leagues, a move that would potentially remove affiliated teams from some markets across the country. What did not appear in the story is that this is probably long overdue. Nobody wants to admit it, but there are a lot of markets out there that can't support affiliated teams or lack the facilities necessary for modern player development.
Minor League Baseball president Pat O'Conner says that the MLB proposal would be "the equivalent of a death sentence" for 42 teams ... but he also said in March 2018 that minor league baseball would have to contract as many as half of its teams if baseball were required to pay players a living wage. There's no reason to assume that the current number of affiliated teams is the correct one, or that the locations of teams and leagues (which haven't changed in over 50 years) are still optimal despite the fact that MLB has nearly doubled in size, expanding further west and south, and considering population changes throughout the country in the same time span. There's a vast tract of ground between favoring the status quo, and favoring MLB's proposal to excise a quarter of current minor league teams from the affiliation ladder.
The fundamental problem for Major League Baseball is that it doesn't actually control the entities that directly influence the development of its young players. Most minor league teams are independently owned and operated, and the leagues themselves are all independent of MLB.
The relationship between MLB and the minors is governed by the Professional Baseball Agreement (PBA), which was last fully renegotiated in 1990. In the interim, the only significant change to the structure of minor league baseball has been the dissolution of the third Triple-A league, the American Association, in 1997, with its eight teams moving into the International League and the Pacific Coast League. Leagues have expanded and franchises moved, but nearly all of this has happened without the involvement of MLB. Since 1997, there have been only a handful of realignments across the full-season A-ball leagues, most recently when MILB contracted two non-viable California League teams and expanded the Carolina League by two.