I'm on the side of having borders like [-----A-----------A------][-----B-------B----] and would prefer intense military situations (or a friendly trade situation) to look like [------A--------A][-B--------B----] instead of [---A--][---B--][--C--][--A---][----B--] or something like that. I think it would give it a way better RPG feel because even close towns in RPGs take a long time to get to one another (ex. in DA Denerim to Lothering).
@Climber
I think that limiting population and having different village types is a great idea but you don't need to have a bunch of small villages close together to make it feel like an RPG, what about the typical isolated fishing villages in RPGs? And you can have one big mining city if you have a close farming village/city (or a friendly one) to ship food to it, but it will be risky if the farming village is destroyed but thats part of the strategy. I also completely agree that the world should only have a couple or few large metrolpolises where developement depends on the location such as: land fertility, trade routes, $ put in, political importance, defence, religious importance, security, economy etc. These places would also be where many political meetings take place (like the united planets in GC2)
On a general note I think I know and like what Boogie is thinking make it feel like an RPG before a Civ game.