If we have a transport ship, and we attach modules ? (like in Startrek)
Imagine a ship that we can't pilot with autopiloting, we can't roll it as the others ship, because every hook between modules have to do a spin effort (resistance bar hook needed in the hud) If you roll too fast, you break the hook and lost the cargo.
The ship have a large space for batteries, and can pull ahead an established weight
(3 ship models, light, medium heavy, example: light = 3 modules, medum = 5 modules...)
There are different cargo-modules to transport different things.
Every module can equipped with 4 auto-targetting weapons so when the player comes attacked, can exit warp and answer to fire or can use part of the energy to activate the shields to defend the cargo-modules.
Players that wants to engage a cargo transport, must shoot to the transport ship, and not to cargo-modules!!
Then, they must use a towing beam or they must have a transport ship to join the transport ship to the column of cargo-modules.

Some example of my idea:
http://linuxgarage.interfree.it/Images/Vendetta/taurusII.png
http://linuxgarage.interfree.it/Images/Vendetta/Cargomodule.png
http://linuxgarage.interfree.it/Images/Vendetta/sample1.png
http://linuxgarage.interfree.it/Images/Vendetta/sample2.png
http://linuxgarage.interfree.it/Images/Vendetta/sample3.png
http://linuxgarage.interfree.it/Images/Vendetta/sample4.png

:-D

That would be too easy to hit. Cargo transport users would tire quickly of getting maimed in their space train.

(Nice drawings though)