If Lucas was brought on to do the first Star Trek movie, he would certainly understand it is not the same thing as Star Wars. He would almost certainly be constrained to tailor a Star Trek film fairly closely to the the television show. The film would have the same basic cast of characters, with the same general personalities and relationships. It would have the same basic back concept (based in "our" future, a federation of planets based on vaguely enlightenment ideals, etc). However, I suspect he might play around with the details of the bacsktory quite a bit such as:
(1) Clear good guys and bad guys - perhaps an "evil empire" the federation was struggling against (in most of the "real" Star Trek films the enemy is not usually a whole society or people, but some sort or renegade)
(2) Some non-cannonical surprises connecting the characters "Jim, I am your father", etc
(3) More acknowledgement and respect for spiritualism and mystery.
(4) More action with clear military/battle resolutions rather than talking the enemy to death
(5) Robots - possibly even one as a main character
(6) More "alien" aliens in and outside of the Federation
Actually, certain aspects of the new movie (the rebellious barfighting young Kirk, the bullied and conflicted Spock, Kirk being marooned by Spock on Ice Planet Hoth to face giant monsters before meeting with an equally outcast Scotty and his Jawa assistant, and the whole prequel thing) sound very much like the kind of directions Lucas might have gone in if he was given the freedom.