This either hints at a darker concept to what Emet actually did in the past, or more likely, you're thinking too much into it. I have major doubts that the writers got that far.
1. I agree about Zodiark. I was quite underwhelmed and disappointed that He was relegated to such a place in the story.
2. Actually I found Meteion and Hermes' pert of the Final Days to be important and part of the story fine. Perhaps it's because I know how Hermes felt on many points, going through such feelings and thoughts myself over the years, and know that if I was to see multiple planets and civilizations eradicated in the loneliness of space ... I'd probably go bonkers too.
3. The thing with Venat is a tricky thing. I do see where she was coming from, as millions of her kind were being sacrificed to make a primal, and I think coming across that last group of devoted Zodiark followers tipped her over the edge. Yet it makes me wonder if she needed to do the Sundering to become a primal as well? I don't know (or can't remember) if they touched on that.
Overall I was pleased with the Endwalker story. I cried a lot and had to pace myself more than other expansion MSQs.
To be fair, I don't think a lot of people would have sympathised with the Ancients as readily if they had looked like they did in Amaurot. I personally liked that version of their appearance, though back in Shadowbringers I remember some people dismissing them and declaring that the likes of Ardbert were 'better' because he was 'hotter'.
On the other hand, Shadowbringers was seemingly designed to build up sympathy and understanding for the Ancients and their plight but Endwalker just tried to dismiss everything that had been done on that front by trying to claim that they deserved it and their fate was inevitable.
It's almost as if someone deliberately only looked at the feedback from those who loathed the Ancients and Garleans to reinforce the silly idea that both races needed to have every possible tragedy inflicted upon them. Something changed in the development phase - because previously the interviews by Yoshi-P stressed a need to showcase the nuance. Then, for whatever reason, they decided to backtrack.
Having seen how petty the writers back in WoW behaved whenever the audience did not respond as they wanted to Sylvanas and Anduin...I do not doubt that something similar plagues this game. Mostly because it's pretty bizarre for the lead developer to try and declare that a major character is a 'good person' for engaging in genocide. It isn't his call to make as to how people decide to read into a character's motives and level of sympathy nor has he ever tried to enforce it for other characters in the past.
Because I've seen people talk about the moon and Zodiark parts a bit recently I'm curious what thoughts people have as to how that bit could have been handled better. What would people change about that one section?
Kind of ironic that the expansion that fleshed out the Amaurotines -- literally -- showing us as the humans they are was also that one that wound up... dehumanizing them and brushing them aside as inferior because of their attitudes and lack of ability to directly manipulate niche feely energy that only really works at full power in space.
Personally I'd compress all of the chores surrounding Argos and the Loporrits-being-sinister stuff, and also the useless 'stalk Urianger even though he notices you anyway' segment. Zenos and Fandaniel arrive later on, and we have more time spent wandering around and talking to the Zodiark souls and learning more about Zodiark himself. I think travelling and arriving on the Moon itself should've also had a bit more fanfare and 'oomph' to it, considering how hard Yoshida was hyping it up and marketing it. As is, the Scions acted like they were just taking a walk in a different part of town than usual. Like, I know you've been through a bunch, but this is the Moon, you know?
Just to comment on this...
Venat was aware of the impending approach of the Final Days and did nothing to mitigate them. She stood by idly and allowed them to happen. If Merlwyb had stood by idly as the Final Days loomed over Limsa Lominsa and then struck it, would she be a heroine or a villain? If she looked into the eyes of a traumatised child who had seen their parents brutally slaughtered by a Blasphemy and told them to 'move on' immediately would she be a heroine or a villain? If she had then decided that the child reacted in the 'wrong way' and inflicted genocide upon every surviving Limsan would she be a heroine or a villain? If she then declared that the Limsans were bad people who deserved their fate and sought to expunge all memory of their existence from the pages of history whilst also stealing their accomplishments and passing them off as her own...would she be a heroine or a villain?
For those who have their answer to the above, replace 'Merlwyb' with 'Venat' and 'Limsans' with 'Ancients'. It works the same!
That aside, Zodiark was a necessity. Without Zodiark, there would be no Etheirys as the first two rounds of sacrifices were needed in order to prevent Etheirys from being destroyed. Venat had no business getting up in arms over the sacrifices as the first two rounds were needed to preserve Etheirys and were entirely willing. The third, meanwhile, was intended to sacrifice a portion of the 'new life' that Zodiark had allowed to flourish so that the Ancients trapped inside Zodiark could be freed rather than left to linger there for all of eternity.
We already know that the protagonists consider being trapped in such a state to be a horrific fate or they would not be rushing to go and save Vrtra's sister who is lost in the Void. Though, as ever, the approach seems to be a case of 'it is okay when we do it, but only we'.
I don't recall him ever saying that, only something along the lines of liking to keep the same face until his current task is done, implying that he took on the appearance of Solus and is continuing to use it for as long as he is meddling in (I'm guessing maybe) Garlean politics, or whatever he considers to be the end point of the current task, but in past "lives" he had a different particular appearance that he would return to if he ever had to switch bodies.
At this point I stopped caring about the story and I'm not sure if I want to buy the third Encyopedpia Eoreza considering even the writers are not bothering to fill plotholes and contradicting themselves so what's the point of buying something that lore heavy.
MFW thinking about the expansion and it's story after beating it
I just wanted eldritch horrors and Zodiark. Was that so much to ask?