This has more to do with mods, in my mind, but I suppose it's suitable as an idea as well. It basically involves being able to select a settlement on the world map, transitioning to it (as you would sometimes do when entering it with colonists), and then altering its appearance to give it greater character and uniqueness. Though for all I know, there's a mod that allows for that kind of thing already. If there isn't, then it would still make for interesting content in the base game. Albeit difficult to implement.