[PvK]

In Proportions Mod, I use organics partly to represent specially trained personnel. Most shipyards have a low organic build rate, so if you want to build elite units, they take longer to build. There are also improved versions of the ship control components to represent extra investment in training and equipment, which is expensive but can push the envelope.

However in general, I tend to think of Fleets as elite commanders, officers, and personnel. The best ones come from actual battle experience, and they can be transferred from ship to ship, can be wiped out but also can survive the loss of a ship, and they cannot just be manufactured, except to the degree they can be trained. So, I just name my fleets things like "Captain Kwok" and so on, and I think that works fairly well.