The way I read into it, MLS is looking to have more control over the development path to the MLS. So they want to have control over the development league of their choice.
To me, Miami, New England, and Toronto have no business playing against Union Omaha level of competition and should be positioned as a stepping stone into the MLS/a place to let players recover after an injury and get back to the MLS. I'm sure MLS isn't much of a fan of this either.
I imagine in a perfect world, MLS teams would want a dedicated U18 league and a league just below MLS to develop their farm system.