[Raapys]

I've always liked the 'Settlement' idea, where you just really drop facilities as such and turn the entire colony into one facility which produces more and more as it grows.

Perhaps as an addon to this there could be facilities called for example 'Focus Field - Research', which would basically let you choose a specific area that colony should focus on. Makes sense on planets with a high mineral rating to focus on gathering those minerals, for instance. Or perhaps you want the colony to focus on building ships, so you build the 'Focus Area' that increases construction for that colony.

About the ancients, you could just pull them back to the stoneage and let them join in with everyone else. Stuff like Organic Technology could be something everyone would eventually get access to, if technologically advanced.