I wrote them about this and suggested it when PTW was in the works. I think it would be great. When negiotating with the AI about cease-fires or RoP or asking them to respect RoP, one could refer to the name of the region, whether it be a lake, a river, Mountain range, etc. It could be a preset list, like with cities. Instead of cities being bartered in trade talks, the different regions could be traded.
I would also like to see Explorers used for something and Scouts and Explorers could be the first to discover a region and name it. Throughout the history of the game, the AI would also refer to those regions either by their name or yours, perhaps based on the culture or power rating of the civ. Even without cities built in that region, perhaps being there and naming it first could give the region a tendency towards the discoverer's civ. Balancing with expansionist civs would be a factor I guess, but it's something to think about.