This is, in my opinion, the weakest part of Rubicon’s current design. I ended up just copying the Asteroids model of infinite waves- if you keep winning, the game never ends (though the difficulty does scale up, but not quite at the rate that you get upgrades…). Quitting feels like just giving up the investment you’ve put in, and there’s no other end condition besides death. In game, beyond survival there’s just nothing to work towards.
Instead of trying to fix this through a save system, I think that breaking the missions up into discrete sets is the best solution. Either Star Fox-style, where you progress through missions until you fight the final boss and either win or lose, or Tower of Goo-style, where you can select and replay specific missions, would be valid choices. A save system would just delay the inevitable existentialist pointless end.
Problem is, these options would have taken a lot more level design time, which would have taken away from some essential core gameplay work. Until a whole bunch more time and resources suddenly get freed up and I’m able to release a patch that adds that sort of metagame, I recommend just playing on harder difficulties where death is more immediately inevitable.