I think a lot of this depends on the outcome of the final battle; there will be time between then and when the new game starts to set up and work out that kind of detail, but it would prrrrobably be good to move beyond aliens with the game's new theme and direction rather than always have the looming threat of the aliens returning. Or maybe we want that threat, but not immediately. ;D

The discussion would certainly happen in-game. I'm seeing it as potentially being a very divisive issue that could split Numbered down the middle; think team "parasites are gross" and team "well if they keep us healthy and make us stronger..." I'm in agreement about some tenseness between humans and Numbered, but that will probably vary by region. I think right now it looks like the new Numbered mecca will be in New Zealand, which is apparently a sort of "safe zone" that's relatively untouched by the invasion, so maybe there people are decently OK with the Numbered but in more war-torn and devastated locales people are far more hostile.