This is all fascinating stuff! Thank you all!
In regards to beginning in La Noscea, I definitely still plan on doing so, but I will probably omit the part about refugees. There are plenty enough people who will need helping there without that plot detail, and it could add an interesting twist to Ul'dah when the party arrives there. For some reason, I missed the detail that Ul'dah was a refugee center during the Calamity, as I had tied it more strongly with the Highlanders' fleeing from Ala Mhigo. I'm just going to have to find a better reason for all of the party to have been in Limsa - not too difficult, as I'm sure at least some manner of recruitment for recovery efforts was out there.
In regards to Mhach, you all gave me a lot to think about. I'll probably hold back and save Mhach for later, if at all - there's plenty of content to explore outside of that. My original intent was going to be to have the 'leader' of the Lambs of Dalamud be a direct descendant of a Mhachi warmage, who was using the group as a means to gain more and more magical power under the auspices of a cult dedicated to Dalamud. He was kind of insane, but in a more Lawful Evil type of way - he thought he could bring back some remnant of his ancestors' power. I might still try to work in a similar storyline, but leave Mhach out of it.
I had forgotten the plot detail about Leviathan destroying Limsa Lominsa as well! That gives me some ideas for how to work in the Sahuagin, and how to begin the Allagan ruins exploration storyline too.
One thing I learned after poking around a bit in-game yesterday - it does seem that the aetheryte network is damaged somewhat, given that Revenant's Toll was taken completely offline by the Calamity. I didn't want to give my players easy access to teleportation until it made sense, so having this actually be something they can work towards might be a good way to encourage them to move around (running protection for Aetheryte reconstruction missions, and facing heavy resistance from Beast Tribes who want to take those sweet, sweet crystals for themselves.)
Again, thank you all!