I noticed when I was cloning factions for when I made my custom civilizations the base factions all seem to have Logistics at the very bottom of the list of importances, I think that might actually be why fleets are not being correctly formed. Not until the Dregin declared war on me around turn 500 did I see any actual fleets just random ones and twos floating around, it was easy killing the Krynn because all their ships were not joined up.
