Since no one has explained it yet, details.
Taking X3:Reunion's main plot as the starter. You start out a lot like Freelancer, a pilot with a ship. There's new badguys popping up and nuking people out of nowhere, a generic badguy. You go through the missions, trading and blowing up pirates to advance yourself, a lot like Freelancer still. Eventually you win and are left with no more serious badguys to exterminate, still a lot like Freelancer.
What's not like Freelancer at all is the system in which the campaign takes place. You have a property management system that lets you deploy ai pilots in multiple vessels. You can buy freighters and run them manually in that management system through orders, or you can pop a higher level trade computer in them and automate the bastards entirely with the click of a button. You can form flight wings, set groups on system patrols, set up mining bases on asteroids, buy factories, battleships, carriers, even obtain a space station for producing ships yourself, all without the use of mods. They have a simulated economy too, weapons are built at weapon factories, using components that come from other factories, built by raw materials mines from asteriods, with energy from solar panel stations being the juice that makes them all run.
Unlike Freelancer, you can build up an armada with your own industrial power behind it and wipe out entire systems in glorious fleet on fleet battles with carriers, battleships, and hundreds of fighters. It's beautiful, although this happens at a couple fps if you're running anywhere near the recommended sys reqs...
With mods, specifically Xtended, the game is pure badass outside of that minor issue I previously mentioned. There's something very empty in beating script driven opponents, if the races were actual sides with their own motivations, I'd be in heaven. With the right mods though, you can systematically exterminate them one system at a time and clear the entire galaxy of all that reside.
Edit: Ship capture! Can't believe I left that out, pilots have a chance to bail out when you kick the crap out of them, leaving you a damaged ship that you can take posession of. Freighter captains even dump their cargo for you frequently when you attack them. Piracy really does pay in X3. 