I can't tell if you want a game where you can fly a spaceship and murder things, or command spaceships and murder things. So here are my suggestions for both:
Freelancer: Fly ships. Buy ships. Do stuff. Meet people who don't own the space station you're on, but have an understanding with the people who do.
Darkstar One: Never actually played this one, but from what I understand it's closer to Independence War than X3. You have one ship, and you can explore space, but you can attach a lot of things to that one ship.
Galaxy on Fire 2: I played the iOS version, but there's a PC version. Basically Freelancer on the go.
Galactic Civilizations II: 4X game. Conquer space. Actually create your own ship prototypes. You don't get to fly ships on your own, but you can make some ridiculously strange races to play as.
Sins of a Solar Empire: A little more straightforward than the one above. Conquer planets. Build stupidly large fleets. Zoom out when your computer strains rendering a hundred ships firing upon a hundred other ships.
I'll also mention Ur-Quan Masters (Star Control II) here. If you're looking for an RPG in space, a lot of games can trace their lineage back to this.
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