MSQ
I have a feeling Papalymo will in fact still be alive because, as the rule states, if there is no body he ain't dead. Regardless of this however its almost certain that his spell will be revealed to have a VERY short timer...and even worse those reinforcements that Ilberd had called in to unknowingly help summon the primal are probably the same ones going after Omega in the trailer. Most likely not only will Nero be the one to suggest using Omega, but the reason the GC Alliance will go with it is to keep the primal out of Garlean hands. Yda pushing that button is probably her atleast trying to keep Papalymo's (supposed) sacrifice from being in vain. How well this works out, well, we'll have to wait and see.
Oh also, you are now thinking about Lahabrea hijacking the primal summoning somehow because of the eyes being used. Which could also mean he will hijack Omega.
Warring Triad
I'll admit to being in the minority when it came to thinking Regula would die as I thought he would live, so hey I was wrong. That said I could see Varis allowing experimental procedures be used on Regula in an attempt to bring him back, OR if he actually isn't dead but is near it (clinically dead or whatever) it would achieve the same thing. This could lead to further Kefka parallels as the returned/reborn Regula would be driven isane by the results...but this currently is idle speculation on my part.
As for our good friend Unukalhai color me surprised on him staying, though I gladly enjoy it! This does make me think that the WT will indeed be required for completion in order to move on to Stormblood alongside Regula's death. Also he for sure will end up allying with us in the end when it comes down to us vs Elidibus, though it wouldn't surprise me if it takes some time for him to decide where his own path will go. This could also help flesh out Elidibus's character more depending on how he views Unukalhai, as an asset or someone he actually cares for.