Use the thrust overrides and you should generally be okay.
Also limit your framerate to 60 fps to be safe.
This is shameful. I had downloaded a 360 controller config, but was not setting it as the control config in the options menu of the game. So it was defaulting to well the default. The 360 controller worked, but the right stick was completely inactive, and the left stick would help with positioning. I could only use throttle. I remembered the importance of straffing and sliding, but this time I thought that I was just supposed to do so while flighting against the throttle. This control scheme would have been great for something like Freespace, X-Wing, or Wing Commander. In Independence War 1 and 2 this left me a sitting duck. Once I actually selected the proper control config in the options menu the right analog stick became used for thruster override. Combat suddenly started to make a lot more sense and became a llot more like I remembered it.