The Federation exchange is a great way to get materials and make a profit. Considering that the Klingon faction doesn't have access to it, there within lies an issue. This might be magnified by the fact that the Klingon faction doesn't have the same looting potential that the Federation does.
I would suggest Cryptic consider making the exchange a universal system for all factions with one common market. It could be something as cannon as the Ferengi are behind it.
Later on, this same game mechanic issue is likely to hit the Cardassian and Romulan expansions. Both are likely to face the same issues with pvp balance that the Klingons often do now.
As such, a large, universal exchange system might make it easier for people to equip now for things that might not be fully developed content. Thus, there might be more balance in factional pvp.
PVE people on the Fed side could make a profit. PVPers on all sides could benefit from their work and provide customers.
Rare stuff like Romulan Ale and Cardassian goods might also go across this market to the Federation. This gives the exchange both a sactioned feel and a Black market edge common in the Star Trek Universe. After all Bones got his stock of Romulan Ale from somewhere.
That's my thoughts. To Cryptic and the player base, I have to then ask. What are yours?
I would prefer the exchanges remain seperate and a new faction, Merchant created that is neutral in the war effort but can travel between the various spacedocks of any faction and buy/sell items there. You could also have merchant related quests and missions.