Just an idea I had... what if instead of just researching Propulsion and getting faster and faster engines, your engines were split into multiple families (i.e. Retro Rockets, Ion Thrusters, Solar Sails, and Jump Drives), and you could only have one of each engine type on each ship? So if you want a really fast ship you'll have to use one of each and let each of their cost/supply/tonnage/etc. advantages and disadvantages average out, but if you want the specific benefits of one type, you'll have to settle for a slower ship overall? To make things interesting, engines would use mQNP-style scale mounts, just so that all ships don't end up the same speed, which would be boring.
Any thoughts?