Ship size?

Yes indeed. I mostly build small and medium hull ships, and just a few "fleet-breaker" large/huge hulls. Medium seems to give the best combo of hit-points, logistic cost and space.

Side-note:

I'm not sure I agree with the concept of the same weapon or sensor unit taking less space on a smaller ship. Obviously stuff like life-support and engines should vary with hull-size.

I should also say that you can build say 5 medium ships on 5 planets and have them in action much quicker than 3 large ships built on 3 planets even though the production cost is theoretically the same.