Duke these are my thoughts about alien game-play:
1) Aliens do need bases on alien planet to accommodate their attacks on it. Some facilities can be changed to follow the alien infrastructure but I do find that overall the buildings could be the same with different looks and titles. Of course big difference is that you have to start with Anti-matter production facility immediately.
2) You start the technology with some of the weapons missing so they have to research them for some time. As for the future, since humans develop new weapons based on both technologies (theirs and aliens) it could be possible to do some research tree following that logic and link those new weapons to the alien side. You also need to realize the humans infrastructure to know which targets to hit that have the most impact to them and help in their faster assimilation with a decisive win at the end on the most powerful nations military bases (namely discover Phalanx bases
).
3) Currency and salaries and maintenance costs; that does need a lot of thought. A hive mind does not need currency or trade. But what it does need to get things done is time and resources. We could replace currency for humans with resources like anti-matter producing facility which will be required to transfer the various goods. Still this needs a lot of thought how to be implemented in the game in a way that feels "philosophical-correct" for an alien hive mind.
4) I agree totally about the freighter idea, sounds superb.
Hope one day in the faaaaaaaar future we will really reach at that point to start building new and various campaigns!
