So, something I personally like is to stay on few, if not a single, colony. Its just something I prefer. Obviously, doing so is quite negative in the long run, having multiple settlements just beats having a single, well developed, one.
So, with that said, I would like some new buildings only being buildable in your HQ, but in return costing cosmite (and maybe populace, basically the cost of a 'settler'?). These could be progressive upgrades, the first one adding a flat amount, the second then adding a percentage, to offset bad sector luck.

How these buildings should actually 'look' (exclusive or stacking for a super city?) and where they do fit in would be still up to discussion, but I think that they should unlock with technologies, maybe even the residential district ones.