Why I think the controls work great for a space sim
When fighting, I don't know if a joystick could have allowed the freedom to change directions and fine tune your aim anywhere near as well as the mouse. If technology is so prevalent in the setting of a space sim, why would you require fixed hardpoints just to use a stick for control. It seems like swiveling guns with a control scheme that truly complements that makes the most sense from a sim point of view.
When trading, or generally flying around the system, it makes sense to be able to click on an object in your "HUD" (sure it's not presented that way, but I feel like it should have been) and have the computer set a course and get you there. Planes and space ships today currently spend most of their time being piloted by computers. Computers control space shuttle launches and re-entries, autopilot handles the majority of your time on a passenger plane. Why shouldn't a flight computer handle "docking" into a trade lane or a space station? And when you can't really trust the computer to handle everything, such as during an intense firefight, see the above paragraph.
Now I'm not saying one is less fun than the other or that people shouldn't be given the choice, I'm just trying to respond to those who dismiss the mouse control as not sim-like. In my opinion, a position can be made for a control scheme like this and it wouldn't surprise me to see space sims in the future adopt a similar control method (although I feel that classic flight sims - IL-2, Falcon 4, etc. -, even including sci fi games like X2 or Tie Fighter, are better with a stick).