Keep in mind that, while I have played my share of MMOs, FFXI wasn't one of them (*flame on*). Maybe my opinion will be valuable for the non-FFXI perspective, and others can fill in with a FFXI-informed perspective.
1) If airships are added, the distance between cities becomes normalized. The current dynamic of Ul'dah being favored because it is in the center of the linear path becomes diminished. Hopefully this will reduce the 'over-centralization' of a single city like Ishgard.
2) The locations of the crafting guilds in various cities (and presumably NOT Ishgard) promotes crafting of the appropriate types within the correct cities. I suspect that as time goes by, more of the more advanced recipes (darksteel, anyone?) will require tier 3 facilities, thus requiring crafting within the appropriate city. This effectively creates more demand for certain products within those cities.
If retainers could more easily be placed within the market area of your city of choice WITHOUT the need to travel there (see previous suggestion for NPC linkshells for retainers), supply could be made to more easily match demand.
3) There are high-level areas all four 'citified' zone. Coerthas stands out simply because it is missing the lower level content (monsters starting around rank 20ish), and gathering nodes of only grade 4 and 5. Heck, there are rank 65 sundrakes practically within walking distance of Ul'dah. Hopefully these high level areas will have high-rank content to go with them, and so this content will be well distributed throughout the continent.
4) Grand Companies will be present in at least the three cities of Gridania, Limsa Lominsa and Ul'dah (listed in order of my personal preference ^_^), but may not be present in Ishgard. Perhaps some other mechanic will take place here, since there seems to be a more 'warlike' vibe to Ishgard, as well as the small keeps surrounding it. Activity around the Grand Companies will draw people to various cities, thus upping demand in those cities.
5) Beastman tribes are present in the three principal city-state areas, but not in Coerthas. Once Beastman-related activities begin, there should be more draw to these cities, and again increased demand for goods.
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In summary, I see two tactics to maintain market activities in the three principal cities:
1) Specialized materials for crafts practiced in that city (e.g. darksteel ore in Limsa Lominsa, rubies in Ul'dah, pieste skin in Gridania)
2) High rank activities based out of all cities, to maintain active player populations and fuel market demand.