5kers thursters are max 150m/s... all snub pirates reach 200m/s or so... so thrusters not allow more chances for docking in a base... as someone said hehehe...
Also, someone said... if remove thursters improve cargo hold, something like 7.500 cargo... not bad at all, that also will can help for bases suplying. Right now... 5000 cargo ships cannot hyperjump in group and the task is turning in a bit pain.
I like the idea about old Barge back!!! hehe I loved it soooo much that super turtle speed... lol
About protection... think also in places with radiation, mines, gases... nerfing more the armor protection would be dangerous for keep traders alive.
In my opinion... dont touch the transports for now... there are other things more important i guess