In some ways, FOTS unit design mirrors evolution - I mean, in some ways detailed enough to be interesting. You've got basic building blocks from which designs are derived. The number of possible designs is much, much larger than good designs. For example, I don't know of many that have a use for a single repair bay. You don't have many hull 1 starships to repair, a single shipyard could repair them and build small things; a single hangar could repair or refit small craft in much greater quantity and carry them too.
Which possible designs are made actual are the result (1) of prior designs and (2) of selection pressures. Prior designs are an influence because they'll determine the player's mindset, what he's got to refit, and what he's built the yards and/or factories to build. If you've got a lot of hull 12 ships, you're going to be interested in hull 12 designs, since that's what you can get out of a refit and you might well have a lot of little 12 or 24 capacity shipyards. This might even be the case, if, starting from scratch with the techs and situation and design doctrine you've now got, you wouldn't build a single hull 12 unit. (Or at least, that was the case with the Rrowlk'aa, over massive changes in the techs available and considerable changes in fighter rules - John Dolan seemed to just scrap and rebuild every time he had a reason.)
Selection pressures keep you from seeing those 1 repair bay designs, for instance, or 5 LRS designs. But they're a lot more organic and less static than those. You want to build a fleet that can survive and compete against other fleets, and that's usually other specific fleets, built with their own design philosophies. Those design philosophies, even for the very same techs, don't reduce to obvious strict optima at any given time, and the collective wisdom of FOTS ship designers - to the extent there's a consensus, which isn't very - changes over time. Your own fleet design is a selection pressure on the other guy's - if he's a specific threat for you, chances are you are for him - and this introduces a continuous cycle.
New technologies can be read as mutations, increasing the part pool. There's a lot to be said for that reading, especially if you follow a policy of frequent tech trades and a large number of modestly funded projects, since either will get you a somewhat more random bunch of techs available. But that still puts you at one end a continuum from some choice to total choice over your techs available. In practice, what techs you get have some relationship to what techs you pursue, and what techs you pursue are influenced by what techs would work well with your existing unit and tech mix. They're not ahistorical resources, but more a part of the same process.
What you get is a fleet that's built from modifications to prior designs in obedience to the dictates of environmental pressures and combinations of existing components and abilities - ship genes - along with the occasional new one, with environmental pressures largely consisting of rival fleets/species.
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