One thing I have thought about doing is, instead of there being a set number of missions, there would be a certain score you have to reach (adjusted for the selected skill level) before the final boss map. That would guarantee that the player has advanced to a certain point before the end.
In that case, though, the scores become pretty much meaningless as a measure of how the player did, since they would all be almost identical by the end of the game. The score measures how long the game has been going rather than the player's skill.
From my perspective, the score reflects only the "luck of the draw" since it is highly dependent on which maps get selected to be part of the mission. I kill everything, so if I get the maps with the most enemies, I get a higher score.
The score can become irrelevant if a person saves right at the end of each level. If they don't like the next level because it doesn't have enough aliens, just re-load, re-finish the map and see what map comes up next.
I do this, but not for the score. I do it in case I get a map I've recently played. Then I can reload and get a different map.
My goal when I play this mod is to try to level up the weapons and get tougher aliens, not so much for the score.
The score can become more relevant to me if, like the boosts the player receives for getting so many weapon progression, an ability increases or a secret level is gained.