Th base idea is good. The actual upgrades need some re-thinking. It's too complicated in my opinion.
For example I'd like the idea to add:
-1 Equipment factory module
To build:
-Weapons for fighters, transports. Similar to code weapons.
-Armour. Even capital. If you collect ridiculous amounts of Ablative armour and such.
Or another idea:
-Smelters:
They would refine ores and He-3. That way - if the base has enough cargo for the process - 1 gold ore is refined into 5 units of pure gold (so the process is worth the money). Or 1 He-3 to 5 units of H-Fuel
Those are my 'under the shower' ideas. But they still need programming and debugging. And still not sure how many of you think they make sense.
I like Kosa's ideas. Those three concepts make sense within the Freelancer universe: weapons, armor and smelting raw materials. Good module ideas.
And I like Phillip's idea as a general concept, but the specifics don't make as much sense in the Freelancer universe. In many other games "research" is about upgrading stuff. In the Freelancer universe research is more about studying anomalies or alien organisms, or developing new pharmaceuticals.
So I would propose that a "research module" allows the base owner to create the most profitable pharmaceutical and medical commodities by feeding in basic pharmaceuticals and some other base materials (probably new ones-- chemicals of various sorts).
Producing these in proximity to some high sell-point could be very profitable for the base owner.
So research would be more about producing commodities than upgrades.
As for the base npcs, POBs are coded differently than regular bases, so they don't have the regular entries in the mbases.ini and their "rooms" are empty. Since changing this would tedious if devs/admins did it for every POB (which might then die) I doubt this will happen.