It would have been nice if there was some more granularity on the affinity scales, so more mundane tasks could feed into them. Terraforming activites (chopping forests, draining xenomass, building terrascapes) could add to purity/supremacy, and subtract from harmony (not sure if subtracting from affinities would work though, as how would it handle upgrade requisites disappearing). The problem with this, though, is flavor. How would you differentiate between a purity act or a supremacy act, with regard to the impact on local environment? You'd have to expand on their definitions a bit to narrow it down.
Purity - do everything possible to turn this place into earth. Terrascapes, clearing miasma
Supremacy - do whatever it takes to survive. Chop forests, boreholes
Harmony - protect and enhance the native environment. Spread miasma, destroy terrascapes, etc.
They could have done more with the terraforming than just a singular 'terrascape' upgrade. miasma should respawn from certain types of native terrain, the invasive species should naturally spread, etc. The impact of humanity on this world should have a much more organic effect than a few tiles done only though the directed effort of the humans. But then, that would be more world building, and not civilization building I guess.
Hopefully a new expansion brings the oceans/lakes more into line as well, because currently, they are essentially mountains that units can sometimes cross. My wish is that the first expansion focuses on making the world more dynamic.