Why not have a wonder for a 'commodities exchange'   build the wonder and every civ er. race can buy or sell and the host nation gets an economic boost.  

Hence, ship construction time is based on assembly and ship yard technology ... resource availability is based on factory output ...

To counter the strategy of resource starving,  have generic building materials be available to every planet, where some planets have a higher resource output than others, but basic materials can't be choked completely out crippling ship building.  

Special resources and the planets that contain them would be strategic and therefore something to fight for.   

General market where everyone goes to sell their goods works. I think the black market is corruption that you build in some else's territory where their corruption come's in as your commerce. This could be added to espionage. Another idea for a general market it could be small wonders that if you build them they  would be connected to the other one's this could also be done through diplomacy. This could also be an galactic council option that can be voted on. This could be an option for alliance or economic treaties. Lets not forget about pirates could also have this option. These could also be trade goods for the ones who don't have these resources until you get the resource on the map. The option I'm talking is about aquiring strategic resources you can't get when someone choked you out by aqiuring all the strategic resources of one type.

Excellent,  the Black Market concept could be use for hostile or enemy races and allied or neutral races would be included in the general market ... trade agreements could be forged to lower tariffs, and prices .. ect. 

It's been a while since I played it, but in Birth of the Federation, dilithium was a key resource in ship production, and if I recall correctly, not every planet could be mined for dilithium.  If you played as the Romulan Star Empire though, you could build a singularity plant.