Basically, why is it that colonies appear on the world map yet never actually interact? Why not have it so there's a option to turn a colony into a faction, thus deleting all of their saves? You could pick a colonist to serve as the 'leader'.
Sort of a 'retire colony' option? Turn them into an NPC group? That would be neat. There might need to be an upper limit on how many factions could be added this way, or else certain menus could get cluttered. Perhaps the game picks the nearest 4 to appear as factions you can communicate with, or randomly selects 4, or whatever.
Yep, pretty much.
Hell, it'd even be useful, since I change mods sometimes and don't want to waste the old colonies...