I like the idea of civilian research facilities as it provides another aspect that could introduce roleplay, as well as make the game somewhat more dynamic.
Perhaps unlike CMCs which are worth 10 mines each, a CIV lab could be worth 1/10 of a research center and have an option to purchase the research output from it, albeit at a higher cost than your regular labs, if purchased the lab would select a project your scientists are already working on and add their output to it. Otherwise the lab wouldn't require any funding and would be left to randomly design components similar to what is produced when you start with pre researched ship systems, but weighted slightly towards making something that might be useful to you, maybe it could compare what's being made to what you already have, and unless it's either very different to what you're already using, range/power wise etc, or if it's similar to what you're using, but with newer technology, then the script rerolls for a new component.
The Lab could be named after one of the companies you've designed a component with already, and maybe it could specialise, for instance if you have earlier made a "weyland-yutani search sensor" the game could later roll a weyland-yutani Sensors research lab, which might design a bunch of totally useless sensors and fire controls, but eventually it might make one that actually fits some need you have, you could then use that system in your designs.
In order to not clutter your class design and ship systems page you might need a new window listing available components from the CIVs, sortable by company and type, the systems should go obsolete after a year or more if you don't use them. From this window you could select a component and use a button labeled "Obtain License for this system" or something, which allows you to use it in your designs, BUT it should cost more than if you had designed the thing yourself, I mean they have to fund their labs somehow right?
For added complexity you might make the CIV shipping companies contract out new ship systems to CIV research LABS when they start popping up, for instance say the AI designs a new sorium harvester which needs a larger engine then any ships the company already has, if there are no power and propulsion labs around then the game just does whatever it is it already does now, but if there happens to be a P&P lab somewhere, then the shipping company sends that new system to them. After the system has been designed then for every ship that company launches using the system the Engine company makes royalties equal to say 20% the cost of the engine, AND you make some tax credits. Then like CMC's or shipping companies they can expand when they get enough capital. Also they become a source of income but only as long as you have a thriving shipping industry. Perhaps you could abstract out the tax income in order to reduce complexity/required coding, also it would allow all types of CIVs to provide revenue not just those being used by the shipping companies.
