Now I know it's not quite the same thing but Mission: Space could act as a glorified video game. We see it in arcades where your joystick controls certain things, and the screen has some degree of variability. As for Indy in Disneyland - There are 3 paths you can take at the beginning but when it comes to the ride itself what is the real difference? Is it just what Indy says to you? Don't all of the tracks converge to the same path rather quickly?
The formulaic Disney ride doesn't necessarily have a protagonist or an antagonist, it just has "something go horribly wrong". Except in the case of Toy Story Mania where they've eliminated conflict (and to a lesser extent story) in favor of interactivity. Test Track also lacks the "something goes horrible wrong" moment. A shallow attempt at it is set up with the barrier test, but aside from the pre-show and the obviously fake (and often broken) demo there isn't much buildup to this portion. Everyone going on the ride is aware there is a high speed section, and that's really where the anticipation build up is, not in the controversy or story.
With Mission: Space, I actually feel the story isn't too far off from being a prototypical Disney story. We have an objective, we're going to Mars, but then we wake up in an asteroid belt, and have trouble landing. What would make the attraction better would be different options at the point of controversy. Ok, we get in the asteroid belt and we have options: steer out of it, shoot some sort of weapon to destroy the asteroids or what have you. Much like the current system, this could also feature the same type of override, but the ride would feature choices with different ramifications. As it continues the ship could be steered to different canyons on Mars with different endings as well.
Now I was told that while spinning, the pitch/angle of the cabins themselves have to be consistent across all of the arms of the centrifuge. I find that somewhat hard to believe, but if it's true, it doesn't mean that the different on screen options couldn't be coordinated with the same cabin movement.