SO, some things that have been running through my head and hopefully aren't just a jumbled mess.
Starting with G'raha Exarch's past/alternate future:
We know the catalyst for the 8th Umbral Calamity is the combination of all the Light from the First being intergrated into the Source coinciding with the release of Black Rose, supercharging it and make it the most deadly biochemical warfare known even to our own world. But what isn't said is who exactly ordered the use of Black Rose. For all the talk some people have of needing to see the nuance of Varis's character most signs point to him giving the order for Black Rose's use. Whether it was a last resort born of his reluctance to bring full military might on Eorzea as Elidibus wanted or because he held back deliberately so as to kill as many as possible to help cause the Rejoining because of his own mad plan isn't known, but it was almost certainly him. Even if he was not the one to give the order he is still complicit due to restarting its production. In this latter case Elidibus was most likely the culprit, either behind Varis's back or possibly killing him and stealing his body to do so.
As well this very well may have been the worst of all Calamities. We know that the after effects of previous Calamities did lead to people warring against themselves over what they thinked caused it (example being the enmity against magic users during the Fifth Umbral Era.) But this was just a slaughter of the worse kind that was only barley avoided thanks to the help of people we most likely will never meet. In paticular is that of Biggs, eight of his line. It should be noted that this does NOT mean FutureBiggs is a descendant of the current one because (as I just looked up before typing all this up to make sure I know what I'm talking about) the first lore book states that both Biggs and Wedge are not using their real names in order to keep the Garleans from hunting there families down for them deserting. He most likely looks like Biggs as a hint to the player more then anything else.
On more character speculation, Estinien most likely never joined the war effort in this alternate future. He only starts helping due to Tataru and Krile tracking him down because they need the help with all the Scions and the WoL being unable to help out due to the First, something the alternate future version of them wouldn't have had to do. Its possible that this change currently doesn't actually change much, maybe in the alternate future Thancred was doing the same thing including teaming up with Gaius to try and stop Black Rose production, but we currently don't know and probably never will. The one thing that probably would have been near enough the same is that if we were going to lose to EldiZenos in the fight even without Exarch's interference, just after a much longer fight, he probably would have saved us anyways. And of course the alternate future proves Exarch's words true, it really doesn't matter whether we would have won or not because Black Rose would have killed us later on anyways. Personally I do still think we could have beaten EldiZenos if the Exarch hadn't cut in, but it doesn't matter in the end.
Which brings me to the next character, Zenos. In the current timeline Zenos ends up going to get his body and kills his father but he pretty much states outright that he only went to do that of his own volition because we weren't around for him to go after/watch. In the alternate timeline there he at best hung back and was content to let us fight our way to Garlemald and at that point would have went for his body, at worst he was an active thorn in our side by trying to fight us in his new body, possibly even body jumping to keep on coming after us. Regardless him not going after his father and his body allows for the use of Black Rose, something he himself doesn't seem to want to actually use. At best in the current timeline he'll keep it around as extra incentive for us to go after him and thus participate in his "hunt"
Now for something a little different lets go back to the Crystal Tower story. In paticular that of Xande...what, exactly, is the Xande we fight? Based on what we learn in SHB Emet was the creator of the Allagan Empire and thus was the original Xande, yet apparently the Xande we fight in CT was supposed to be his soul in a cloned body. My own theory is that, given that Emet never actually died Amon and the others involved in bringing Xande "back" thought they succeded when in fact they really just managed to create a new sentient person. As a result the notreallyXande thought he was, and since he had no memory in between his "death" and his "rebirth" he thought there was nothing after death when in reality it was because he couldn't have any memory of an afterlife he could in no way have been a part of. Makes his fate all the worse honestly.
And finally of things I currently remember and thus able to write down, a little on the Blessing the WoL has. Our understanding of it prior to SHB was that it allowed us to go beyond mortal limits, but now that we know more about the world, Source and Shards all, it seems that isn't about going beyond our limits so much as tapping into the power of our original self. Even at level 80 the Amaurantan shades say our power of creation is very low, showing just how far we can really go when it comes down to it. As well we most likely manage to tap into it further at certain point of the story, in particular when Hydaelyn is helping us out during the fight against Ultima Weapon and Lahabrea. As well it seems that while we and Ardbert are supposed to be part of one being that our souls are still able to be separate even after he gave us his power given he rejoins his friends in the credits. Ardbert also wasn't the only one that people have said is very similar to us, Tenzin being the other one I can think of currently.
And thats my rather long ramble in the spoilers. I have some more thoughts in regards to Hydaelyn and Zodiark but for now I'll keep them to myself. I believe 5.X patches will bring more to light in regards to them and thus I will hold off on too much speculation there till we get through at least 5.3