Many of those continents may as well have been unoccupied though, given how low the population density was; i.e. they'd be better represented in CiV by empty land rather than by land belonging to a civ.
Or at least land that might have other civs' cities around it but remains somewhat uncontrolled would make more sense. It's a conceit of the game that civilizations require cities, so maybe if there was some incentive for the AI not to go spamming them every four spaces, it would work.
As for resources, there already are biomes, and those of a given type do tend to cluster (luxuries more than strategic). Maybe if it were a little harder to trade between civs on opposite sides of an ocean, where you can't send your entire empire's worth of steel to the other side of the globe based on the vague notion that you maybe saw a French guy once, plus either less-packed cities or the chance of stealing some land when you found your own, there would be more reason to colonize in order to get them.
I just think that in a game where civilization = giant cities, it's correct to say that the land belonging to the Inca, the Aztec, the Iroquois, Songhai, etc. should just be empty space with a smattering of barbarians.
I mean, I guess you could dial it back and say the same thing of England, Germany, Spain, and so on.
What if you could set a game where you get three categories of AI opponents? Say you have the human players, the AI civilizations, but then a gaggle of AI "civs" who have all the same stuff as the ones you aren't using in the game, but have some kind of handicap that makes them lag behind in tech, border growth and city construction? If those clustered together, you might have a better "colonization" scenario, where you do have to take
some land from people who are already there, but you aren't hitting a Wall Of Danes as soon as you cross the sea?