Both control methods sound promising, but I'm afraid you underestimate the capabilities of the pilot.
Let the computer handle stabilisation alone and give the pilot full control over the thrusters - or the overall working of the thrusters.
I got this idea from an arcade game I played a really long time ago (only once and I was 12!).
You don't distribute the controls among the sticks or the pedals, instead you make a control system where the joint movement of the control devices creates the current thruster configuration.
What do I mean?
Let the pedals control the nosal thrusters of the fighter - your legs are bolted to the pedals, so you can both push and pull them - you'd need that anyway in zero-g.
If you puch the left pedal down, the left-lower-nosal thruster kick up, if you lift it the upper thrusters will.
You control the verniers with the sticks - they will be just a tad more complex than what you have right now:
If you pull a stick towards yourself the lower thruster on that side will kick in, the other with the other stick.
Pushing it will start the upper thruster.
If you push the stick to the side 2 things can happen: if it's a to the side where the stick is, the thruster on the opposite end will kick in and slide you, the same with the other stick.
The system may seem redundant, however it's TRUE, that you can't both slide and spin with maximum thrust at the same time.
To achieve a roll on any axis, you'll have to use the controls among the axis oppositly or use just a single control on one side.
To slide you use the controls in conjuntion.
If you want to both slide an spin you'll aply more thrust on either side of an axis.
Throtle is either controlled by torquing on or both sticks or pushing them forward Gundam esque.
I'll drow a representation once I got my webspace working.
