I know it's a very old question, but I wasn't lurking the forums then. I figure I'll answer. My ideal setup is as follows: Stick with Z twist and thumb stick in right hand, throttle with thumb stick in left hand.
X - Yaw
Y - Pitch
Z - Roll
Y - Strafe forward/backward
X - Unused
Throttle - Throttle. D'uh.
X - Strafe left/right
Y - Strafe up/down
Control X and Y aim of movable (gimballed/turreted) guns
I will prefer to stick with fixed weapons where I can, so head-tracking is less important. A second thumbstick on the joystick is a decent substitute for head-tracking, as the primary thumbstick on the joystick is used less often. Because the X axis on the joystick's thumbstick is unused in this control configuration, a self-centering analogue wheel is actually a better option for me, as it would be easier to push-click (for Boost) while finely controlling its position.
The thumbsticks on the throttle and joystick are interchangeable, but I think it is easier to mentally manage the way I have listed.
I used a setup almost exactly like this with my Cytek Cyborg Evo and CH Pro Throttle. However, my CH Pro Throttle doesn't detect its full range. My CH Pro Throttle can't go to 0% or 100%, even when I calibrate it with that in mind. Its range is more like 1.5% - 98.5%, which means I can't hit full throttle or stop without special means. Other than that, it's button positions are fantastic and its calibration program, while ancient, works well enough. My Cytek Cyborg Evo was a pretty junky stick, centering imprecisely every time, requiring huge dead zones, and it was unstable. Additionally, the built-in throttle tended to auto-detect for any axis binding when setting up my controls, which was infuriating. Finally, the 8-way hat was of course digital, so I had imprecise control of forward-back strafing. Anyway, despite the flaws of my last HOTAS setup, it was actually surprisingly easy to manage 7DoF like that (the extra DoF being the throttle). 9DoF using head track is also hypothetically simple, but I have never done it.
VKB is the only company that has offered (or will offer) products that do everything I want, and at a high quality standard. I am eagerly anticipating your throttle. Just please place the thumbstick in a comfortable resting place where your thumb can easily use its full range of motion.
Ideally, I'd like to use the thumbstick on the throttle for walking, but CIG doesn't have that as a bindable option. It is theoretically a good idea; lots of quickly-accessible buttons, a thumbstick for nuanced movement, and a mouse for quick aiming.