I really loved how Perpetual had decided to do it (based on historic soft canon and our ideas too, imo).

There would exist in STO:

1) UFP Civilian and Government Economic systems & the 'Credit' or C.I.C. (Common Interplanetary Credit: Established in the Articles of Federation in the Star Fleet Technical Manual (1975) (one of the best selling, biggest money making Star Trek books of AAAALLLLLLLLL  time.) 

The articles establish payment of credits to crew for services rendered to the UFP through Star Fleet service.

Used for personal transactions. Can not be used to obtain (military grade) empire or faction items outside a black market.


2).The Latinum based economic system in some other areas of space bordering UFP space.

3).Prestige. To acquire all ('military grade' )empire and faction items.


How do you have civilians, pirates or fringe groups without the above. Not everyone wants to be in empire service. 

Civilians and pirates need ways to get military grade equip.



Sounds like Cryptic is close to that too.

I'm pretty sure Cryptic hasn't said anything about using a "loot" system. I also think you might be taking the term "credit" a bit out of context. A credit isn't always a unit of currency, for instance if I'm in school and I have a project due, I get credit for turning it in on time. A credit in this sense is just an acknowledgement of work I have completed. Try this wording and see if it seems a little better...

Transporter Privileges or Replicator Privileges....:)

Gozer

 "Privileges" may work well if one is into semantics, but transporters and replicators take energy to use, and replicators also need matter to convert. The reason Voyager's crew  were on replicator ration's was because of the serious need to conserve energy and matter on the ship.
 The use of credits in the Federation is a standard for a few hundred years, and one would need these credits to 'purchase' replicator 'matter' and ship energy (dilithium, et al).
 The use of these credits, in the context that Cryptic used them above;

You can’t simply decide one day that you want a starship and then get one, you have to have enough credits for that.

 My reasoning on this is that sufficient credits would be needed in order to have Star Fleet build the ship for you, and also credits would be used to upgrade the systems after you have received your ship.
 My original concern was with this:

 

There will probably be episodes where you get to commandeer starships from other factions.

 This  "comandeering" an opposing factions ship and getting credits for it. This is likely the main source of in-game currency (my words) for the Star Fleet faction. Federation traders and miners will earn their own credits in their way. The Klingon Faction will use the Latinum base (I presume) and also have the "comandeering" system as well.