Major Spoilers for all Expansions - Some general things I didn't understand

[Arlythe]

4. I'm going to need a little more clarification, because I don't remember the Omicrons resurrecting anyone.

Of course.
It happens in Ultima Thule during the Omicrons' tribe quest. You restore the café we find in the MSQ right before Alphinaud and Alisaie lose their bodies to form the stairway.
In order to reopen the café, you need customers, so you start resurrecting the Soldiers, the Grebuloff and the guys whose name slips me right now (They summon that Sphinx like Boss, Ra-La, at the end) you can see their worlds of during the dungeon "The Dead Ends" and find out what they loved to eat the most.
One by one they start using Dynamis, recreating parts of their homeworld and even create more of their kind.