Most RPG series by the end of the PS1 generation were adopting the Indiana Jones style map where their was a map and dots you could visit that were actual towns and dungeons a la BoFIV, Suikoden III, and Persona 3/4. I know Shin Megami Tensei III: Nocturne had a real world map but it was a very barren place (which fits nicely with the games main themes) which though having a few cool optional points of interest was not as engaing as mid-FF world maps. Suikoden V's map is pretty epic.

If there was one thing I would love to explore using a World Map, it was a minor feature from VIII and IX that I felt never got due justice. VIII had the trains that kept going on schedule and Lindblum had airships flying in its airspace to dock in the castle. I would have loved to see World Map with more interactive elements like these. Could you imagine flying your ariship and actually having to be careful not to collide with other airships? Hell, actually running into other people on the world map would be pretty cool even.