I liked how the local auction houses in FFXI worked early in the game. With certain items only available in and near certain cities it allowed for trade between the cities and forced people to visit other cities or ask friends to pick up items when passing through. The problem was late in the game's life people began to centralize around Jeuno, making that the only AH ever used and killing the economies of the other cities.
I think you may be able to fix this by giving each of the starter cities their own AH, then link the centralized city's AH to one of those cities in a cycle. For example, link the centralized city's AH to Limsa Lominsa's AH for a week, then the next week link it to Gridania's, then the third week link it to Ul'dah's, then repeat.
I think this could keep the starter cities' economies from dying late in the game, while still allowing the advantages of having separate economies for each city.