I seen an older thread about a similar thing, it gave me and idea
What if we could manu three different ships, one from each major faction (milanar for uit, siepos for serco and prosus for itani), by completing a mission tree, and then anyone can choose what to manufacture, however missions for different factions would require at least +200 standing to manufacture the ship. They probably only have to be manued once, similar to capships then could be rebought at Xang Xi/Corvus stations.
The ships would be different, depending which variant was made. The siepos one could be a prometheus-like ship, based on hive guardians(orne or arklan guardian, for example), with moderate cargo, heavy armor, and a prometheus-like port layout, or two large and one small port. The prosus ship could be based on one of the hive assaults(could be similar to a dentek/prosus assault), agile, fast, small and lightly armored like a fighter. The milanar variant could be in the middle, would be less armored than the serco one, but with the most cargo space, and have a wraith or warthog like port layout, this one could be based on one of the transport ships(like the aerna transport, but probably shorter, and even smaller), or in guardians.

Flying such ships could be cool, and would be a nice addition for the game.

Big surprise but +1