I had a quick glance at the rules and overall you came up with a simple and workable system. I especially like the rules about the captains' abilities, which is I think what differentiates Trek from a lot of other games. I also like the way the ships move; it is very simple yet I think it accurately depicts how starships move on the show. The only thing I've noticed was that you didn't use the canon figures but that's ok if you wanted to depict an abstract system, like the CODA RPG. Also, I don't see much difference between photon and quantum torpedoes, as I'd expect the latter to cause more damage. But overall nicely done.
"Oh better far to live and die
Under the brave black flag I fly,
Than play a sanctimonious part
With a pirate head and a pirate heart!"