I was thinking one thing that would be cool for the endgame would be an inverse of the regular game: the geoscape goes to Mars, and you end up as invaders much like Aliens on Earth. Maybe having to build a few bases and attack some Mars bases before finding the real final Mars base. You'd think aliens so advanced would have a lot more than just 1 base...
Of course, this would probably be a hell of a lot of work, and is well outside the scope of a ruleset mod...
Otherwise, it would probably be best if the final base had its own map group so it didn't have to use the regular Alien Base elements (allowing different rooms than it). But this is a mod feature rather than an endgame feature.