A more detailed naval construction system. Actual parts like engines, main guns, secondaries, armor schemes, not just tch levels. Each base hull type (DD, CL, CA, BB, etc) having a certain amount of space which would be taken up by your various systems. Make it a balancing act. Want to overload the armor protection? Why, suddenly you don't have room for that big engine you need to make 28 knots. And add inefficiency penalties so players aren't trying to overmaximize the amount of shit they cram right up to the hull limit. You'd still research the various areas, but it would be to unlock a few new breakthroughs and to make the different parts more efficent (improved shells on the guns, a more efficient engine that gives you the same power output on less space, etc)
For players that don't want to deal with that, just have historical designs usable by default, along with a few planned-but-never built ones (the Montanas, the Maltas, Graf Zeppelin, Sovietsky Soyuz, etc). Having played Galactic Civilizations II, in which there was a far more complicated system and the AI had no problem designing decent ships, I'm sure it's not impossible to make an AI capable of doing this.
And have a tonnage limit or something based on your IC and modified by shipyards/shipbuilding research, to more accurately reflect actual capabilities.