It really does feel like at some point you lost the story and just refused to pay any attention afterwards. Lets try to TLDR through some of those questions atleast. Zodiark is a god created to fix the celestial aetherflow, effectively creating an aether shield to ward off the dynamis bombarding etherys. Afterwards they tried to sacrifice even more people to recreate their perfect utopia. Hydaelyn sundered him (and the world) which made him very weak. That allowed her to magically imprison him in the moon.
Hythlodaeus had already sacrificed his soul to Zodiark, she couldnt have saved him. While emet selch got away from the sundering on his own. The blue meteion is the one that didnt personally get corrupted by despair, the network just took over and drowned her out. When the network is destabilizing she can make her voice heard again but not for long. Ultimately the network's despair is defeated and she can fall silent. Why would she be mentioned again?
The person turning in the foundation is the blasphemy in the caster role story, I take it you just havent done that quest line.
Leaving Emet-Selch, Lahabrea and Elidibus unsundered is in parts time travel weirdness, they always needed to be there for the story to play out like this but who is to say that hydaelyn even had an oppurtunity to sunder them. There is nothing inherently stopping from the story playing out in a way that doesnt include ascians or rejoinings. My interpretation is that she never had the chance to sunder them and therefore we always would have had to deal with them.
Emet-Selch probably liked Venat (in his own cranky way) but her betraying the convocation put them in direct opposition.
Hydaelyn wanted us to find out the pieces of the puzzle for ourselves so that we would have the clarity and resolve to face despair itself. So that we would fight for ourselves and not just because someone told us to. Borrowed convictions crumbles easier in the face of overwhelming despair. Meteion also wasnt really relevant as long as zodiark was still alive.
"Hear, song of creations end. Feel, the sorrow of hope's demise. Think, and find your way in the darkness." It's a response and preperation for meteion when she says "I wish to hear your words, share your feelings, know your thoughts". We wont defeat her by power alone, we need to conclude her mission with atleast one hopeful planet.
Y'shtola never died, she used crack teleport magic twice, got heavily injured by zenos once and terraformed the path with her soul like the rest of the scions in ultima thule. Was she close to dying multiple times? yea sure
I am not surprised you didnt care for moenbryda's parents, you clearly didnt care for the story in general at that point. It is an important step for urianger tho. There's also a side quest about papalymo's dad. Those people still exist and telling the parents of your former comrades of their death shouldnt be a light hearted scene.
The lopporits only make sense if they are cute and approachable. They are supposed to welcome the people onto their new home on the moon, do you want the housekeepers to look approachable or do you want them to look like behemoths? At this point I get the impression you want the story to be bad to have excuse for not paying attention. You're just taking story points and ask 'why do they make sense, i dont want them to'.