It seems more clear.

The two groups are on two separate places, just the "eleven" (who have been plugged out of reality in the Vanguard story) are not around in the MBL Universe, having been placed in a different, altered reality. Right?

What do we want for the MBL

I have two suggestions:

•One is the one implied by the first post of MBL one: Promethean City is a dirty and dark place, that hides many secrets, cospiracies, corrupted politicians and such... a cancer growing on the side of Thunder City, a shiny place that has been an heaven for metas since 2001, in the core of an America that hated metas.
Now that metas are not actively hunted anymore, just Thunder, of any place, what was a flag for metahumans freedom, has become threathened by something only our heroes can fight.

•The other is something we talked for sometime with Pro, and it's to make them a global protectorate, something JLA-Autorithesque, or, to stick to the HR-Vanguard universe, a new Strikeforce.

My preferred choice would be going from the first scenario progessively to the second, having the MBL gaining global status thanks to the good work they did in Promethean city.