The capital ship number is dependent on the how many captains have been trained. Its not a number for the number of ships you can have, but for people trained. So that part is actually in the game.
I found Leaders in MOO3 to be a complete waste of time, since they always died of old age or assasination pretty quickly. I cant see a purpose for them in Sins. I dont recall moo2, been so long since i played it.
You could add fleet admirals to capital ships, and various levels of training that make a fleet more effective. However, since a lot of people dont use fleets, since this feature has so many things wrong with it, I would think that admirals should act on all ships in the gravity well. More than one admiral there, then the highest ranking one gives the orders. Or you could have multiple admirals in a gravity well multiplying the effects.