If I had to say the one thing I always wanted to see in an RPG-style game... it'd be long-term consequences for player behavior.
I'd like to see a game where colonies rely on the player for growth. Say the colony is able to grow only so much before they need x resource from a certain time period which may or may not be on the continent. The player can choose to get the resource, which expands the colony, or ignore the request, which incurs a long-term consequence for the colony (people start dying, that sort of thing, Civ style).
I'd like to see a game where colonies rely on the player for protection. Say there is another group of survivors out there that also is trying to make it... and they see the colony as a place to obtain easy resources. The player can choose to defend the colony or ignore the request and the colony is either able to protect itself or become abandoned.
I'd like to see a game where the size of the colony matters. Say the player needs certain resources but the because the colony is too small the player can't 'fuel up' there. This could cause the player to invest more into the colony. Or the colony is unable to assist other colonies because it's too small. For example, a colony at level 3 can spare so many colonist to create another colony (and is reduced to level 2 or has to pay some other long-term cost).
I'd really love to see a game where colonies develop independent of the player. Say the colony is able to research certain spells that the player can't obtain himself or is able to grant certain benefits based on its size. That'd give the player a reason to invest in the colonies and revisit old ones.