right so i've made some more progress, out lined fleet limits for the imperial navy and i've decided that the merchants/rouge traders fleet will be turned into a sort of imperial sub-faction used in specific senarios (or if you just feel like it), i'll be doing this with the tau who will also have a merchant navy type sub list
pirates - options to take human, ork and eldar ships (but not ork and eldar) and chaos cultists (not full on marks of chaos but sort of a mild version)
tau - similar to imperial navy - have main list and merchant sub-list
chaos will have its own raider oriantated list
necron/tyranids will be there but I'm not sure on how to make them fit in with the pirate
Eldar/corsairs/dark eldar, well they were pretty much pirates to begin with
when i get round to the senarios i'm going to try and make a story driven campaign, as you play the campaign the fleets get larger and the result of some battles will determine which senario is next/advantages and dis-advantages