Not really a 'sim' but modded Freespace 2 is easily the best I've played for combat, controls and storyline. Truly amazing feeling dogfighting for your life and then in comes a massive cruiser with beam cannons to save your bacon (just the sound of them warming up has me jizzing my pants). Definitely superior than Freelancer in those regards, although you'll have to live without trading.
In fact I'd say for a 90s game, FS2 is arguably as close to perfect as any game from that era. Everything just feels right, the controls are complex yet intuitive, the mission briefing voiceovers give you goosepimples, you feel like part of something bigger than just a lonely one-man-band existance that many games feel (squad communications etc)....