I agree with Yukonsam. I know it hasn't been fully realized yet, but I do like the idea Cryptic has had about trying to make each faction different. That's one of the things I've always hated about MMO's....each faction usually feels just like the rest. The only thing that's usually different is how the factions look.
Having a civilian faction sounds like a great idea to me. Iíve always wanted a game like privateer/freelancer set in the star trek universe. You could have the merchants that produce goods in the manner suggested by Trace_Thorne (a good idea btw). And for people that still want some action, maybe there could be a mercenary class that can be hired for various reasons. They could be hired to fight for a major power, or by the merchants to protect the ships transporting the good they've made. They could even be hired to take out/raid a merchant transporting goods.
What could make it real interesting is if these civilians can be hired by ANY side at any time. So one job you could do for the Klingons and the next for the Federation. Iím sure some sort of standing could be set up that could make life difficult when dealing with a major power if you do more work for an enemy power.
All this could even open more PvP opportunities for the major powers. Set up some sort of patrol route missions to protect player merchants. A civilian faction has the potential to satisfy so many players that feel there are things missing from the game.
Most defiantly, I would go for a 3rd party faction... Hell even Section 32 would do for a great third party. they are still federation, but since they are a spy organization, they get all the neat toys, and can fly whatever they want.
As for real crafting...
Would love to be able to actually customize my weapons, take a phaser pistol, and add on a targeting chip, and a high intensity spectrum filter to make it fire faster in normal attack, and hit harder with it's secondary attack.
Mixing and matching parts from various weapons we find in our travels to create one-offs is a good idea, and I would love it.
Hopefully the crafting system is still a work in progress. It's a bit limiting in it's current state.
As far as brainstorming, it might be interesting to be able break down dropped/looted items into base components to be used to craft or modify other items.
I am a starship captain... I do not need to moonlight as a tailor. Or collect a bunch of trash to combine with other bits of trash to create a new piece of trash.... cant yall just play the Memory Alpha game and be happy...
I for one dont miss "crafting"... or the inventory micro management .
Since there is not really big point in crafting unless there is some loss in game(and right now we have non)
I would suggest start with basics - implementing fuel and ammo.
You run out of Dilithium your ship will not be as effective ....lets call it emergency mode.
You can eighter buy fuel or mine it yourself
(yeah i would love to just run out of fuel and have to send a distress call, but causal players would not be happy i guess)
mining materials - manufacturing parts - assembling ammo parts
you run out of ammo - you cannot fire torpedoes and mines