Sorry for the lurking, but happy to hear the idea of Xenonauts 2.
In the question of story I wouldn't worry about it. Every time Civilisation releases a new version it doesn't rewrite every story from the start. In that same way I see this as being a similar format. You can have an entirely different attacking race but without the necessity to start from the end of Xenonauts (1).
Full 3D - I like the idea of 3D but I'm hesitant on the output. It would make it considerably more straightforward to set up mods. Oddly enough I really enjoyed the Commandos 2 & 3 style which mixed decent 2D rotating backdrops and 3D character sprites.
Aliens - This idea, yes. Have the option of different invading super species, different tactics and capabilities.
One other things is scenarios. Situations where you have specific maps or outcomes that are required.