Here's what I'd like to see in a trek strategy game.
- Dozens of races from all sorts of eras, but you can play them radically different, like how you can play Mayans in Empire Earth and dominate the world, but customizable as you start a game: imagine seeing the Federation as a monarchy instead of as a republic.
- Diplomacy and Espionage much like Civilization 4, build alliances, or lull someone into a false sense of security. Sabotage key production facilities to hamper a response to your invasion.
- Research and Production ala Civilization 4, imagine if the Federation developed cloaking tech from the very beginning, or if Hydrans researched photon torpedoes.
- Tactical Combat like in Masters of Orion
- Characters that augment ships or stations like in Star Wars Rebellion, or to serve as system admins, like in Masters of Orion
- A fully customizable server, so you can set certain rules on your server. Change the entire research tree if you'd like.
- Ship design: you start with a researched hull, and that gives you a certain number of slots. Put whatever modules you like into those slots (as your research allows). Come up with a class name and viola. Better research makes better modules, and refit your ships with upgraded modules when they are within reach of a drydock. Research into ship hulls also introduces newer hulls. an Frigate-2 is going to have more slots than a Frigate-1 hull.
- Web-based interface - you can log into the server from a mobile source and play your turn.