Len,
as of right now, the ride appears to be the same each time. Guests are given tasks during the flight (basically pushing buttons and using the joystick), but their actions do not really make a difference, i.e. if they don't do what they are asked to do the ride will do it for them. I suppose there is a possibility of installing alternative missions in the future, but considering that this has not happened with Star Tours or Body Wars, I wouldn't expect this to happen anytime soon.