Trek Wars adds Star Trek Factions into Empire at War. Forces of Corruption. You can play new campaigns as galactic conquest and fight with each faction in Skirmish against each other, Star Wars vs. Star Trek
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Federation Starship
I like the four nacelles on any ship (*cough* Prometheus *cough*) especially in an RTS game. They seem to give the ship some real 3-d depth even when playing on a 2-d grid system. (Refering to the fact that ships can not go up or down very far. The whole game exists on but a single plane.)
Always liked the Constellation, just hope it's equipped with phaser cannons :)
It looks exactly like the apolo class but it has four nacelles instead of two.