It may be cool, but I don't think it is a good idea for RTS. A good mod should have a large variety of units and weapons. But in Star Trek, as far as I know (I am not really familiar with it, but from forums I have learnt a lot about it), there are only ships of more or less the same size, firepower and strength, and there are only two kinds of weapons: phasers and proton torpedoes. That would make the game dull and boring.
Unlike Star Wars. I really want to see Star Wars: War In Space for Spring, with X-wings, Executors and every bomber, corvette, cruiser and star-destroyer in between. And the Death Star
