Let me first say that I accept that this game is a Star Trek themed MMO and that gameplay is accordingly MMO'd (groups of NPCs within spitting distance do nothing while you eliminate their comrades etc).
However, I have done a several missions which are distinctly MMO and not Trek - killing all the smugglers, wiping out the Romulan medical research facility (come on, that is badly scripted - THE baddie should have killed the last Romulans, done evil chuckle and exited stage left) and one where brave, fearless Klingons attacked an unarmed Princess!
Anyways, a lot of killing and no prisoners...
So, how about a capture option when a target is exposed? All it needs is the 'melee' button to flash, walk/sprint over and rifle-butt/punch the target. Instead of vaporize animation have beam out animation instead. Simples. Player choice - good Fed/bad Fed.
Oh - some enemy ships surrendering/warping out of combat would be nice (possibly an option to beam over survivors?). I must have destroyed the Klingon Fleet 3 times over.
On balance I'm enjoying the game, but it needs more Trek and less of the obvious MMO gameplay.