Its really interesting to me that you’re really attempting to make the system organic, that was part of my issue with Civ is the world itself once its generated is reasonably static apart from the units/cities but as you say there are a lot of different things that have happened to the Earth in terms of Climate, I think having to work to actually sustain your civilization, by battling against the elements, is what Civ was missing that Alpha Centauri had that I liked, even in Alien Legacy you had to actually work to keep things running where Civ will happily plod along without too much human interference. I guess its more akin to a game like Simcity, that’s why I brought up rivers but I can understand that the scale is quite different and that didn’t actually cross my mind 
The main thing I was thinking was for flood plains where the extremes of both flood and drought can have a lot more impact, if you built a city close to a river for example and it swells that might cause flooding or even outbreaks of disease if the river doesn’t flow.