The Metro should limit the number of true "A" teams in the area, at the most 4-6. The 2 big organizations in the SJ Metro, and may 2-4 other teams. The way to gauge would be, only the teams who finish in the top 4 of the Metro will be allowed to register A the following season.
I think it is silly to use fiat to limit teams at any level anyplace, because it is self-correcting. Non-competitive teams don't last.
But if you ARE going to limit them, it would be absurd to grant the "biggest organizations" an automatic waiver. Big is often better, but not always. And NO organization should be guaranteed self-perpetuation just because they are big.
I would assume that you see that if only the top 4 teams from the "A" metro can register "A," you can never add another team to the list, since only "A" teams can enter the "A" metro. And so you'll always have the same 4 teams. Unless one folds or has other troubles, and then you'll have only 3. Bad plan.