I have never attempted a mod, and so I have no clue if this is even possible, but I thought I would toss out my idea anyway. I'm sure you'll let me know if it's impossible.
Could you keep the number of engines the same for all ship sizes but add another component that is necessary for them to work?
Perhaps this component could be called an "ion generator," and you would need more of them to power the larger ships (one for an escort, two for frigate, three for a destroyer) etc. Each one would cost a certain amount of resorces (perhaps high on rads, medium on mins, and low on organics) and take a certain amount of supply. They could be part of the propulsion tree, and they could become more efficient at higher levels (Ion Generator I costs more resources and uses more supply than Ion Generator II). That would give players an incentive to move up the propulsion tree - otherwise you would be powering your larger ships with fuel-hogging low-tech "ion generators."