I wonder if you'll have to exchange thermal clips in your phaser?
Using the Mass Effect style COULD still work for a Star Trek if they did this right. Assemble an away team with a cross-section of skills (Medical Staff, Research, Engineers, Security, etc), explore unknown situations that don't necessarily have to end in combat if you can determine what the situation is before things go out of control.
ME 1 had planetary exploration, afterall. If the Star Trek game's approach was to have encounters with aliens be potentially something other than "shoot somebody in the face" and "a cow steals your money", you could remain true to Roddenberry's vision. Of course, it might not always be POSSIBLE to end certain encounters peacefully. If I had a say in the development, there'd be at least one time where two possible dialogue options would be "We come in peace" and "Shoot to kill".
You could also modify the Paragon/Renegade meters to determine how much or how little your captain piddles all over the Prime Directive. Do you follow the Prime Directive or save that infant who's about to burned alive as a sacrifice? What happens if a crew member says "Screw the Prime Directive, they can damn well court martial me!" and intervenes against your orders?
Heck, imagine, instead of Paragon and Renegade, they had Starfleet Integrity and Crew Integrity? Order your crew to let the infant be burned, and kill the mutinous crew member, and your Starfleet Integrity goes up while Crew Integrity drops. Some decisions could gain points in both, and other decisions could lose points in both. Flout Starfleet directives too much and you could get relieved of command. Infuriate your crew too much, and their stray shots might get steadily closer to your back during a firefight...
Of course, this is almost certainly going to be an action game where the developers will feel that the Star Trek label means that they don't need to break new ground (or do any substantial QA testing), but there's always a CHANCE that this could be good.
Hopefully the developers will forgive me if I don't pre-order this one, though.