I figure nothing would be cooler than modding a current skin or creating your own, then tossing in your own rules! Imagine, Cyborg dinosaurs, or even dinsaurs as barbarians! Pteradactals, with machine guns! Or, aliens land, and start causing all manner of ruckus, first by messing around with our environment, then by harvesting us for food! Or, they could be peacful, just exploring the cosmos, and its up to you whether or not to be peaceful to the greenskins or not, perhaps allieng yourself with them, and having them as an ally in future battles!
I think the KDF and/or NIF files that are used for the units and unit animations aren't open to the public. You can modify the DDS files, but when I was dealing with them they were a bit chaotic--I mean you cannot really tell what they are going to look like unless you can apply them to the structures (NIF, I believe).
Admittedly, I know very little about all of this, but have just gained some experience when I adjusted the DDS files for some new resources.
One of these days I'll make 501 posts, and you won't have to look at my silly little diplomat anymore.
"Oh my God, what a fabulous room. Are all these your guitars?"