Ok so, loot sucks. The best gear you get from STF's is junk.
How about this.
End bosses of STF's have a chance (20%?) to drop a ship part. That's right, you know that Imperial class ship you bought on the C-store? or the Heaphastus? Screw the C-store, and add the parts as drops to the bosses. (Ok, it's a bit late for these since people have spent C-store points on them already, but maybe you can just refund the points I dunno, but you can do it for all future ships you add).
Obviously, it is not realistic, how could a borg demi-queen be flying around with some Cruiser nacelles in her pocket? she can't. But it's a game and people need a reason to run end-game content.
A lot of people (most) raid in WoW for the awesome looking Tier gear you get, so you can make your character look awesome and cool and show off to all the noobies in cities who didn't beat the boss yet and get the cool loot that you did. There is none of this in STO whatsoever.
So, add ship parts to bosses... unique stuff.. screw adding them to the C-store, give them to bosses as loot and people will run STF's till the end of time to get all the ship parts they want to customize their ships.
For example, have the Tactical Cube in Infected drop a random (Cruiser/Escort/Science) ship Hull, have the elite tactical borg guy on the middle of the ground bit drop a random (Cru/Es/Sci) Pylon, and have Manus at the end drop a random Nacelle peice or something. Or just have ship parts drop only from the end boss, I don't know, i'm not a game designer (though I ought to be).
You could even extend this to cover things like cool new outfits that aren't in game yet. Again, not realistic because there's no reason why a borg would drop some uniform from the 29th century or something (although you could explain it away by saying the guy came from the future to the past to investigate something and the borg caught him off guard and assimilated him but I digress)
Edit: Forget them dropping the actual parts, just have them drop a "Schematic" or something for the part, which you take back to Memory Alpha and build the ship part with anomalies. Much better. This way it can tie-in with the upcoming improvements to the crafting system.
Heya, I agree with you there. Some items are fine in the C-Store but should be some ways to get unique ship costumes via other means too. A few posts have gone up about your basic idea. Check out my suggestion here --> http://forums.startrekonline.com/sho...d.php?t=147488