I hate to use it as a reference (because yes I know this is not FFXI), but I actually found myself using Jeuno and Whitegate less and less as a main "home". I based myself in Sandy (my starting home nation) because I could easily access my Outpost warps, pay a small fee to get to Whitegate if I needed to or even catch an airship if I had time to spare in order to get to Jeuno. I was RDM and WHM mainly so of course I also had tele's to get around.

With the server search function for players seeking etc, it didn't matter where you were really trying to put a party together- just set a place to meet up before heading off.
And yes, I would really like to see linked market wards so that Ul'dah is not necessarily seen as the main hub for buying and selling.

I think personally if there was a designated "Home Nation" mission/quest strand similar to FFXI where you could change your allegiance and complete all three, this may encourage the completist players to try all three cities and spend time there.
We only have Anima to get around right now, but I know for a lot of people this doesn't last. Once airships and chocobos are introduced (soon!) this will help to improve the situation.
But, I would also like to see some sort of "Conquest" events for your Nation put in- i.e. node/outpost warping for a fee once you have been there or done a supply mission (similar to FFXI), points you could build up for fighting with your Nation's seal on to buy items or buffs, and maybe even a Garrison event (but better) to try and inspire some feeling of loyalty to the town you choose as your Home.

As with FFXI this still will not entirely solve the problem of trying to repopulate "disliked" places, but with more dungeons/events spread out with their entrance near each different city it might help a little to redistribute players across the map.