One thing that I would really like to see is a sort of hybrid between Factorio and a colony type game. Imagine that instead of crash landing by yourself, you crash land with an entire group of people that you have to protect and provide for while you bootstrap yourself up to getting everybody off planet. For those who don't like biters, it can provide another means of making pollution matter. For those who do, it adds another interesting complication.

Along with that, I'd like to see more green energy. Wind power, for instance, could be an early game technology that competes with boilers. Naturally it would need to cost more and / or produce less. Perhaps also geothermal power that must be generated at a particular location.

Of course, more could be done with water. Boats, offshore resources, aquatic biters? Depletion of water resources so you don't have a one tile pond cooling 4 nuclear reactors? Or making the water less useful the more polluted it is.

So many possibilities.