Real life engines have worse power-to-weight ratio as they become bigger. That means a Mazda RX-8's engine has a 50 times better power-to-weight ratio than that of a container ship. In Cosmoteer it is the other way around: The bigger the thruster, the better its power-to-weight.
Why do I mention this? Right now the only right decision is to use the biggest thrusters you can get, since they provide more thrust per credit, more thrust per battery and more thrust per ton. Now if the latter was no longer true, what would mean? In Cosmoteer power-to-weight is directly proportional to acceleration and top speed. If the huge thruster's power-to-weigth was made worse than the large thruster's, it would be slower to propel itself. Sounds bad, but a thruster is never alone. There are reactors, CRs, crew quarters etc. that all add to the overall ship weight.
Eventually it adds a new design choice, where you have to estimate how much of your ship's weight will be thrusters. If you ship is mostly thrusters, use the smaller ones! If you have a heavily armored ship, use the larger ones. Just like in the introductory example of the container ship and the car.
Still a bit vague? Let's say you have two thruster choices and 1600 credits you plan to spend on thrust:
Small - 400 thrust - 2 tons - 800 credits
Large - 1000 thrust - 10 tons - 1600 credits
Which one is now the best option? It depends. If the rest of your ship weights 20 tons the options play out like this:
2 x Small = 800 / 22 tons ~= 36 power-to-weight
1 x Large = 1000 / 30 tons ~= 33 power-to-weight
The small thruster wins!
Now let's use them on a heavily armored ship that weights 100 tons:
2 x Small = 800 / 102 tons ~= 8 power-to-weight
1 x Large = 1000 / 110 tons ~= 9 power-to-weight
Now the large thruster is more cost efficient!
I think this adds a nice new design decision to the game using the existing mechanics and would give smaller thrusters a new life as the best option for fast ships.