It's funny, I agree entirely that the world map system is probably going to change for the reasons specified in the OP. But there is absolutely no reason for it to do so.

Game mechanics that worked in 1997 still work in 2015(ish). There seems to be this assumption from a lot of places (including I think sadly, from SE themselves) that you're going to have to change things because big Cloud/tiny towns would look silly. But we've already seen modern games utilise exactly this sort of scale change and nobody blinked an eye. In Mass Effect 2 and 3, you take control of a Normandy scaled to be larger than planets. You can fly around entire solar systems in seconds. Type-0 HD of course had a pretty typical (if barren) overworld. It's fine.