I'd recommend Bridge Commander if you can find it. It's pretty rare now, but it still a good game. And it's got a large mod community so you can get pretty much any ship you like added to the game's skirmish mode. You can control the ship from the bridge, giving orders to each crewman and watch the action unfold on the viewscreen, or you can have a ship-view and take on the enemy that way, targeting key systems and the like.
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Starfleet Command-Empires at war...was a great series of games...lots of mods and enhancements..i think they made 3
For the consoles...i have for Xbox 360 Star Trek Legacy...very good....its got a story that starts with captain archer and involves Kirk,Picard, and i know they have voyager and others involved with the story....its pretty good...they might have it for PC