That's a really interesting idea!
I was pondering another idea: make large ships take longer to charge up their jump engines to retreat. Ships below cruiser could take their current amount of turns, cruisers and additional turn, and everything above and additional 2 turns. This would give a real niche to smaller ships that are otherwise outclassed in straight fights to act as raiders and opportunists, that can attack and retreat safely if the enemy sends reinforcements to defend while en-route - while fleets of big ships actually need to worry about taking casualties if they get into a bad engagement.
I'd also like to see ship rotation for larger ships more costly in (so that smaller ships getting behind big ones is a real risk!).