Endless incursions? Legendary Battles?

I like the combination victory conditions idea.  I think you should make that it's own separate idea.

Others have definitely mentioned the idea of an extra-galactic intrusion for end-game.  Devs have mentioned that they will be developing narrative elements for the endgame.

I didn't play endless legend, so I can't speak to translation of its ground combat mechanics into ES2.  If you could be more specific on how it would diverge from the current system that would be cool.

I was thinking more along the lines of having distinct ground troops, and even city management on planets that you have yet to fully capture.  So you'd be playing a mini version of endless legend, until you've gotten control of the planet, each time you came in conflict with another race over a planet.  You'd need to capture territory, build cities, etc. until you have full dominance over a given planet.