I’ve made a few suggestions regarding how to make a real “base” work (most recent being the one about a second reality bubble for the base), which would be the first step in any such thing as you’re suggesting, and faction and improved NPC interactions are certainly desired by the devs (from what I’ve seen and read).
Certainly, having some optional late-game goals built in to the game would be nice.
That said, I’ve seen official statements that no “undo” is planned or ever desired by the devs - the world has been changed, and there’s no “fixing” it, no “win” condition. Personally, I’d like there to be some way to “win” against at least one faction, though (say, perma-killing all the fungus, maybe).