Well, it depends what the possibilities for control are like.
If full "Newtonian" is possible, I would have 8 or 9 keys in an extended WASD to control the thrusters, and an analogue control for orientation - mouse or 1 handed joystick with lots of buttons for weapons etc. I would also hope that it is possible to switch between different bindings for different tasks e.g. scooping cargo vs combat. I wouldn't require analogue control of the thrusters at all, just max on or off. I would probably never use fly-by-wire mode, at least in combat.
If the control system turns out to be rigidly "fun" i.e. spaceplanes with no Newtonianness allowed, I really don't know - though with such a limited subset of motion, it won't be hard to come up with something that works.
I'm certainly not going to start buying a load of flight-sim gear that I won't use for anything else! I get images of some posters here surrounded by thousands of pounds worth of flight-sim equipment sitting in the middle of it with their captain's hats on. If such gubbins gives a player an advantage in combat, well, I guess I will just end up ignoring combat as much as I can and focus on trading and exploring. If it does work out that way I predict it will reduce the appeal to the average gamer.
Anyway, the fact that an Xbox 360 controller has been mentioned gives me some hope - I would prefer one stick to control orientation and the dpad (or 2nd stick possibly) to give me directional thrust in the flat plane of the ship, with roll and up-down on say the shoulder buttons.