Took me a long time to get this to written format and out of my head. Not because it was complicated but because I've been busy with CC and moogle tomestone farming. Game is to fun. But anyway. this is my thoughts on the potential future. It's a bit wordy.
Thoughts on where and why we go to the southern continent. (This is entirely speculation and nothing to currently prove any of it):
During a time before Fandaniel decided to travel to Garlemald and help Zenos, he was working under the unsundered to prepare for an eventual calamity on the southern continent. A number of Allagans were put in stasis after the beginning of the calamity that ended the Allagan empire.
Fanadaniel, once Amon had revived those in stasis and convinced them to resume the conquest that they had once been the core reason for them being there. While they lack numbers of pure blooded Allagans, they have the creations and the science to create more. They create husks, soulless bodies that use the Aether from the aethereal sea to power them.
The pure bloods have implanted themselves with technology to control the husks. In an effort to reach a more direct connection to the aethereal sea, they march on the world tree where Tiamat and her brood now rest and recover after the fights on Eorzea. While the locals are fighting back against the Allagans, Tiamat asks for help from her brothers and the Scions.
Estenien goes as part of his new mission to protect the dragons. Y'shtola goes because the world tree is a convergence point of the Aether streams in a way similar to Silvertear lake and may offer a way to traverse the rift between reflections. During the travels it would be possible that two husks have the souls of Emet and Hythlodeus and these two have broken away from the control of the Allagan Empire.
References to past FF games:
The husks would be a nod to black mages from FF9 where they didn't have souls but were created by the villains of the story for a purpose. Having two or three that break from the group would again be a nod to Vivi from 9.
Assuming one of the major fights would be the leader of the Allagans with all his implants, the boss could be similar to Vayne as "The Undying" in FF12.
Since the Allagans are tapping the aethereal sea to power their creations, one of the dungeons may resemble a Mako reactor from FF7 and bosses may be Allagan versions of Airbuster and Proud Clod. The people of the southern continent that protect the world tree may live in a canyon area that separates the forest from the badlands area around it. This would be Cosmo Canyon.