This suggestion is fairly simple and short. Add a weak shield generator on each cargo/transport ship. If you refuse to do this, then enable Engineering and Command ships to support the convoy with their auras.
Eclipse Launcher should also be able to heal the cargo/transport convoy. If you implement shield generator, you can exclude those buffs and heals. You could also implement both options.
Based on my observation there are 2 minor or major issues, which should be corrected, because of randoms. You must decide, if you will add shield generator to enemy convoys as well in PVE and Invasion.
Rank 10-15 PVE scenario only: (if you wish to add shields to Crimson Haze Assault Squad transport as well, then go on ahead)
Pirate Base scenario - round 2 (difficult, but manageable with randoms)
Processing Rig scenario - round 3 (very difficult, loss of at least 1 convoy occures in most cases with randoms)
I would like to ask the developers to implement either a feature (PVE only) that you can heal any cargo/escort ship with Eclipse Launcher and Engineering auras.
Command modules, like speed buff should also affect the transport speed in general.
If 1 transport collides with another destroyed transport there should be no damage done to the 1st one at all. Destroyed debris gets moved away.
However, I am hoping that you will at least give small boost to them, allied/enemy transport/escort cargo convoy with 0 pts of resistances against all 3 kinds of damage types (Thermal, EM, Kinetic).
Recommended shield hitpoints: 10000 pts. only
Regeneration of the shield: 100 pts. only
Resistances: 0, 0, 0 (they could vary)
With respect, Koromac