Just spitballin' here, assuming that terrible ideas are permitted.
A couple times, I wanted V2 to have a "beat-em-up" play mechanic. Throwing punches, kicks, simple combos instead of spells. Or both!
I'm not sure if there's much appeal in an aftergame, but like with my suggestion for V1's endgame, it might be interesting to discover, across an ocean, a "new world" continent that has the appearance of having developed independently, that is now a rival to your continent. I do say this not having beaten V2 yet, though.
This would be a different kind of strategy game, since you'd now have the elbow room to build up things back home without getting smashed, you'd be getting attacked from the coastlines, with periodic drops in the middle of the land. You'd be protecting and developing assets you already have, so it's less of a scramble than before, while undermining and eventually toppling the works on the other side.
I guess you'd have some new offensive units and abilities, etc. for making and establishing beachheads on that other continent. And you'd dispatch folks on missions on this other continent and so forth, while carrying out your own special missions, with levels more bent on exploration as with V1, or perhaps shorter and simpler levels... not sure about this bit yet.
And then there'd be another final boss to contend with, sort of a wicked witch of the west component to old 'Monica.
(I'm mostly thinking about easy duplication of assets and possibly code here, though of course I'm not a programmer and know not of what I speak.)