The Pirate Cartel layer lends itself to being modded quite well, off hand, perhaps its possible to use the Pirate slots for different 'factions' within an empire eg. in Federation space, we might find Vulcans, Tellarites, Andorians, etc.
Another possibility is to use the cartel layer for non-military or commercial traffic for each empire simulating some kind of economy or universe in the background (and not using up valuable slots in the shiplist with freighters without having to remove them), and so on. This would work particularly well if SQL ever works for OP.