I really hope they add other forms of transportation soon. We really wouldn't need any adjustments to the anima system if we could ride chocobos or carriages or something. If they adjust it too much, by the time we finally get chocobos no one will ride them if instantly teleporting is more convenient. Even just an automated travel system that's not necessarily fast would be nice so that you can set it to go and then take a break, rather than controlling your character for the whole walk.
Anima regen would be ok if they had chocobos and airships implemented so i don't think we'll see a change in this for the long term, maybe something short term though?
The devs recently said they're changing it by the end of the year. They're cutting the cost of the "Return" option in half (1 anima instead of 2) and adding a feature where you can set up to 3 "home points" and use the Return feature to travel to them. So as an example, you could set your home point at each of the three cities and travel between them for 1 anima any time you want. Or, to put a slightly different spin on it, it would save you 20 hours of recharge time to travel across regions based on the current cost of 6 anima/trip. That's just an example. From the sounds of things you'll be able to set your home points at any camp or city.
Actually the costs for the three "favorites" is going to be halved, which we can assume means 2 within the same region and 3 for going to another region since they're 4 and 6 now.
As for the 3 cities not being the focal point of XIV, I agree. They are currently but as the game progresses I highly doubt they will be, but how much of the game world do you honestly think S/E will allow us access to by the time the patch comes out? Until more of the world is made available to us, the 3 citys will more then likely be everyones 3 choices.
That depends on how much you personally need to travel to all three cities. Once you get to rank 23 you can do rank 30 regional leves, and there are two aetherial gates per region for these. That means six leves that can be undertaken from the same city. I could see people choosing a favorite in the further camp so that it only costs them 3 anima to get there instead of 5, if all they are focusing on is battlecraft leves. Crafters may be more inclined to use all three cities due to the random factor involved in their leves.