The idea for this is closely related to my commerce rework, but I decided to make a separate topic for it.
My commerce rework idea involved making commerce a one-of-a-kind industry, and I was thinking why not have more unique industries. The civilization games have structures called wonders that have very powerful effects that can only be built once (some only once per faction, and others only once in the entire world). I figure that concept could be adapted for this game as well. It could make the core worlds feel a bit more unique and make colonization more interesting as you try to work out the best places for certain unique industries that you might unlock via exploration or quests. Stuff like the planetary shield already feel like they would be good candidates for that.
Lore-wise, I feel like the lack of understanding of domain-tech would result in this happening, i.e. some structure that can't be replicated because it's no longer understood.