Big Z,
Love the passion on your hypothetical 40-team baseball majors/minors.
The Brooklyn AAA Yankees affiliate thing is off the realm of possibility though because of how the territory rules work.
Yes, if a higher league comes into a territory, they can boot the lower-level team from the territory (after buying them out). For example, the Denver Zephyrs of the PCL, Triple A team. Denver got an MLB expansion team and the Zephyrs were sold to be moved to New Orleans. But it's not a contentious "This is MY territory, I'll fight you for it!" The Zephyrs owners simply realized they could no longer make money in AAA baseball in Denver if there's an MLB team in Denver; so they cashed out.
But the Yankees can't pull that move in Brooklyn, because the market already has a higher team than AAA in it: Themselves, AND THE METS. The Mets have veto power over any team moving into the area by being an MLB team.
In the late 1990s, Mets wanted to put a minor league team on Long Island and the Yankees said no.
The mayor of NYC wanted development in Staten Island and he went to George Steinbrenner because he thought a minor league stadium and Yankees farm team would be perfect. Steinbrenner wasn't thrilled with the idea, but since he wanted NYC to buy him a new Yankee Stadium, he went along with it. He was expecting the Mets veto Staten Island as retribution for the Yankees' Long Island veto, but he'd get a new Yankee Stadium, so he said sure. But the mayor knew how to win over the Mets owner, who grew up a Brooklyn Dodgers fan.
So he brokered the deal: The Staten Island Yankees, the Mets get the Brooklyn Cyclones, and each get new MLB stadiums. (Then 9/11 happened and paused the MLB stadium component for 8 years or so).
