The storyline is definitely going to go back to your home city in some form or another. Whether this entails the story splitting up again or all players resolving the issues of each main city, we'll have to wait and see.

As far as the Limsa story line goes we have tons of loose ends to tie up. Sthalman, Seal Rock, that mysterious Elezen, the Sahagin. You think they're just going to leave all that and just abandon it?