I just miss my moogles.. and Yda..and Papalymo
You will still meet all those people. All of the early quest lines converge into a single story line. From that point forth, there is essentially zero difference between the three cities in terms of which one you started in.

If it really mattered to you though, you simply should have chosen a class that starts in that city. It's not like you can't just immediately swap classes to the one you want to play as soon as you log in.

For example in 1.0 i had face option 1 and nose option 3, in ARR i wanted the same options but they look a bit different; but during the re-customization picking 1 and 3 made it look like the 1.0 version and not the ARR version. This only happened if you were changing appearance and not if you were making a new character
This is one of the bugs they were talking about (I think) and for this reason you will probably get a second chance to fix it.