Ron describes it very well! Yes by ship design I mean actual component changes for a hull type and not spending time painting them and adding spoilers

So just like Ron describes! Perhaps a new Tech Tree called Modular Technology??
1) So you research the basic hull.
2) Then you can research modules like shields, engines.
3) Then you can put the modules in the hull slots.
4) Save the design for next time

5) Produce!
So! just like now you have Fleet Points which determine how many cap ships and other things you can have, same for Module Points which can determine what modules a Modular Ship can take.
I really don't think a modular/slot method like that would take very long times since it is just extra researching and building options. Maybe cost more and take longer but that would be the price of modular ships. So you could spend the time and resources on the regular pre defined ships or instead invest in modular ones, so it sort of balances out.
Just one example! Say you want different defense platform instead of Missile Defense around your planet.
1) Research "Modular Defense Platform"
2) Research "Modular Laser"
3) Produce a MDP, and then "upgrade" it with the modular laser.
4) (save the Laser Tower design)
5) Produce Laser Towers as you would normal installations.
See, it wouldn't take such huge times? Yet it could add so much variety as well!
That would really nock my shoes of if something like this would be made for Sins witch I already find as one of my absolute best games ever!
Mush like one of my old times favourite games: "Imperium Galactica II - Alliances".