Simply put, the best thing we could hope for would be BioWare making a Star Trek rpg using the Mass Effect 2 engine.
The trick for any RPG, even an "Action RPG," would be getting the "World Building" elements right with just one two hour movie's worth of content to go off of. Yes, certain content from the Prime universe can be carried over, but doing so is still trickier on the storytellers, I think, than either a totally new world in which you can do whatever you want (Mass Effect), or an entire universe filled with lore all of which you can echo in your game even if its in a different time (say, KOTOR).
An Elite Force style FPS lessens some of the need for "World Building" (still need visuals, though, and there may or may not be enough of them for Star Trek XI to make a game out of). But there is another problem—FPS mechanics have moved beyond what they were in the Elite Force day; now there's—
- A lot of explicitly "military" squad tactics, which aren't present in Trek in either timeline.
- A lot of "physics"; manipulation of the game world. Say, the use of "cover" in Gears of War 2 or all the barrels in Halo 3 or the Force manipulation in Force Unleashed. I don't know that any of this makes sense in Trek.
- Better AI. How will Trek fans react to enemies that actually hide and stuff instead of coming out in the open to be slaughtered by Our Heroes like all Trek enemies?