"second would be for different aliens (and graphics)"
That would be a neat expansion I agree. The new types of aliens could be more tough and come into play in later stages of the game, where if you have "emancipated" a lot of their nests they would start an offensive against your CIV attacking everywhere where territory has not been takes by any of the CIVs. I am thinking on Blue Gender style extermination attempt against human beings with living alien tanks bursting through defenses and swarms of tough bugs darkening the sky and the only way to stop them is to field a strong counter offensive against their huge nests towering like hills near your borders.
It would enable Firaxis to roll out an expansion with relative low amount of effort since implementation of new alien units is probable easier then for the player and the usage of the already in-game scripting function could take care of the invasion. This would also deliver at least partially on the interactive aliens promise (at least they would react in a meaningful way if the player would go out its way on killing them)
This is also something GC3 could also contemplate: have a kind of apocalyptic event where one of the races goes berserk (kinda where humans are heading in the plot) so if certain circumstances apply all races have to fight for survival together making them almost instantly allies as a nice twist 
