Don't get me wrong, freighters should have pretty decent defense, but they need to be slower than they are now and their armament should be weak. Right now the Rheinland Humpback has so many powerful weapons, it's practically a capital ship! Not to mention Freighters have the advantage of having most of their weapons turret mounted, so they can fire directly behind them. I don't think you should take that away, but it just makes them all that much more powerful (and yes, I know a heavy fighter can take out a freighter, but in terms of the actual NPC pirates, the freighters are too strong).
Personally, I think the coolest thing would be to make it so there's more crossover between ship classes. For example, the Rhino could have a small cargo capacity but have stronger weapons, making it almost a mini-gunboat. Meanwhile the Dromedary would have a huge capacity for cargo, but be slow and have less powerful weapons. Cargo capacity should also be tweaked across the board. Based on the models it seems to me that the Clydesdale (Bretonian) freighter should carry the most cargo out of the house ships (less than the Dromedary), yet it carries only 125!!! I have no clue how they decided to make the Humpback have the biggest hold, because it certainly doesn't look the part!
Anyway, my personal recommendation just for the freighters would be:
Rhino- least hold space (80), most maneuverable (compared to other freighters), fastest, best weaponry and shields. (you could actually sort of dogfight in it)
Humpback- best shields and hull strength, fairly slow and unmaneuverable, pretty good weaponry (equal to Rhino), decent hold space (125). (it's got good enough weapons, but it's a sitting duck).
Drone- fairly high hold space (175), fairly fast, decent weapons, weakest armor.
Clydesdale- second highest hold space (225), fairly slow but more manueverable than the Humpback, weaker weaponry, but still decent defense.
Dromedary- most hold space (275), slowest, least weaponry, not great, but still decent shields (so it doesn't just blow up all the time).
Anyway, obviously you're going to do what you think is best, this is just my personal input.
As far as the Transports go, PLEASE include these as pilotable ships! Adjust the capacity down to make them in balance, of course, but keep in mind they are super slow and have no shields. Also, the Trains don't seem to be able to enter trade lanes, they just have to use their cruise engines (at least from what I've seen, I could be wrong about this). The super transports can carry a lot, but they're super slow and pretty weak to make up for it (in fact, they might need to be beefed up a little bit or they'd be totally unplayable since they'd die in half a second in a pirate attack).