Although the indication is the game is "final", there's still some critique that I hope will improve future games.
The game design seems to imply that your final score will be based on your skill and/or making effective decisions to deal with situations that arise. However, this does not seem to be the case: Most of the score is based on factors that are random and beyond the players control, regardless of skill or choices made. It's more a game of random chance and often choosing the "lesser of multiple evils," but still penalizing the player for the random chance to begin with. If the goal was indeed to evaluate skill and decisions made, you'd need to change how the score is computed--most likely a sliding scale.
For example, the black hole scenario: Calculate the worst and best possible outcomes, have the player make their choice, calculate the results of the choice (which may still include random factors, i.e., "luck"), and then compare it to worst and best. A result closer to the "worst case" suggests the player made a poor decision, while closer to "best case" means a good decision. Accumulate (or average) these values to use as a modifier to the final score. Thus, if a player had really bad luck and comets smashed the seedship around, damaged everything to below 50%, yet they still managed to guide the ship to a paradise planet and start a successful colony, they could still score high to reflect their "skill" at managing and guiding the ship through random disasters.
It's still not a perfect way to score, but it's better than just "throwing the dice" to determine score.
For myself, my highest score to date is 10042. Yet, that run didn't leave me feeling like I actually accomplished anything--I just got lucky and quickly found a suitable planet. Another run only scored about 4000-something points, yet I felt much more like I accomplished something because I was able to manage crisis after crisis that left the ship barely limping along, and still find a suitable planet and start a colony that could survive. In between these two, I had many runs where I just gave up, and colonized the next planet I came to just to end the game and start a new one--yet most of those still scored more than the 4000-something game.