I think you summed it up quite nicely. I've too grown weary of the game as of late and I believe it is in no small part because of the repetitiveness of this task. Perhaps in a future update EA will realize this problem and make the option for automation in the future? Heh but that's wishful thinking.
Overall I just play till I get too fed up setting up colony after colony, then I quit for a few days.
Unlike the other bars in the game, I think the space bar with the ship moving along the progress bar only stands for your distance to the center of the galaxy. I noticed it jumped all over the place when playing around in jump gates. The closer I was to center, the further my ship was on the progress bar and visa versa.