I've been on Mission Space so many times in the past 12 months, I've lost count. Has to be at least 20-25 times. We do green because my wife isn't one for spinning much. I agree the line is very much hit or miss. I've seen it as a walk on, where orange barely had enough to fill the group of teams and we were in the green pre-flight room with one other couple. I've also seen it with 45 minute wait. I think a lot depends on weather and other rides. If it's raining and/or Soarin' is down, then it gets really busy. If it's sunny and everything is operating, it's not as bad.
Spaceship Earth can have a very similar pattern. It can be a complete walk on, or it can be a 30 minute wait.