I actually ditched mouse control in the beginning and been trying out various combinations of controllers including joystick (Saitek Evo), SpeedPad (Nostromo n52) and footcontrollers (FragPedals) for the past week. Neither combination a huge success, but I guess with practice I could be decent.
Then after reading this article and figuring 'why not', I gave the keyboard+mouse combination a second try - and I was immediately able to get past the first beginner/tutorial combat missions
Mouse actually works great and delivers much more pixel-precise control than the joystick. Granted, I haven't used joysticks much since the Atari 2600, Amstrad CPC (my first Elite experince

), Commondore Amiga (Frontier) aera, which of course explains why I'm very rusty with these things. Mouse OTOH I'm using daily for work and games (FPS), so it just feels more natural - to me
The mouse is a Logitech G5 which only has a few extra buttons. It's locked at 2000 DPI and very high cursor speed. I tried out various suggestions for mouse setup, and came up with the following combination of each which works brilliantly for me:
Mouse axis: Absolute Pitch+roll.
Using Absolute setting and high mouse speed, a slight inch movement is enough to pitch and roll at full speed in any direction, while very small movements give you pixel-precise adjustments. I tried out Relative, but it's useless because of the need for endless scrolling. I tried Pitch+yaw and using keyboard for roll - but this left me without an analogue roll and didn't give me the precision I needed. Same thing when trying using keyboard for pitch.
Mouse buttons 1+2: Yaw
This last controller change finally gave me the slight sideways adjustment buttons where I needed it. I moved primary + secondary fire to keyboard instead (currently SPACE + Left Ctrl)
Yaw into roll: Off
Mouse Deadzone: About a quarter up.
Mouse Force: About a quarter up.
These zones will need slight tweaking depending on preference. When I initially tried mouse control I made the big mistake of setting deadzone to zero, figuring it'd give me more control. However this meant what any slight mouse movement got translated into action, making it impossible to keep the ship steady. As someone else already wrote, Deadzone tweaking is key to using mouse.
Anyway after a little tweaking maneuvering is now fast when needed (ie. sharp turns), yet slow and precise ie. when aiming.
As for the rest of the current mouse configuration (though I'm still evaluating this):
Mouse wheel: Throttle control, 25% increments
Works very well (ie. two. ticks up for 50%, two more for 100% etc.). Still, I'm considering moving throttle to keyboard.
Mouse wheel click: Speed Boost
Seemed like a logical place to put it give the wheel is used for throttle. If I move throttle to keyboard I'll probably move this as well.
+/- DPI sensitivity buttons: Thrust up+down
Since I've locked the mouse at 2000DPI these buttons were free for use.
Mouse wheel tilt left/right: Thrust left/right
Again, just because they were free for use. I haven't really done much combat testing using the directional thrusts, so I haven't tested these assignments much either. Might be better on keyboard.
Mouse thumb button: Toggle Flight Assist.
This feels like the right place for it.
As for the keyboard, it's used for target selecion, weapons fire and all the rest. As noted I might switch all throttle/thrust to keyboard and the probably move the target selection function to the free mouse buttons.