I do think this is well thought out. The larger V-base would be the only one with the re-arm pad. In order to kill the rearm facility, you would have to kill a specific hanger, all of the fuel bunkers and ord bunkers (you could even add some, if it is to be larger than the current one we have). Add more acks to the large V-base as well.
The medium V-base could stay the same as it is now.
the small V-base could have 2 ammo bunkers, 2 VH's, 1 ack and 2 manned acks.