Let's play a game: Save the Ancients!

[LilimoLimomo]

Let's exclude the Zordiak hypothesis, because they would only have become slaves of the primal, therefore extinction would be better.

This is an excessively fraught claim for a few reasons:

First, the idea that it's better to die than to live as a slave is incredibly subjective. Let's not pretend for a second that being a slave isn't awful, but history shows that there are many people who preferred life under slavery over death. And of course, there are plenty who preferred death, so let's not forget them. Of those who chose life, some eventually lived to see a future that while still not perfect, is certainly better, and has hope of becoming better still. Which is to say, it is incredibly hasty and unwise to force your personal feelings about whether life as a slave is "worth it" onto an entire population of diverse people. Every individual deserves the chance to make their own choice on that matter.

Second, the Ancients didn't become slaves of a Primal. For all their talk of tempering, most if not all of the Ascians who get enough screen time to be developed as characters take actions that go against the resurrection of Zodiark in important ways. Like, Fandaniel literally kills Zodiark. There's no slavery going on here, nothing close to it.

I'll say that from the information we've been given in the game itself, I am not convinced that Zodiark was necessarily a bad idea.

After all, they are the true inhabitants of Etheirys, because nature created them like this and not with a thin ether like the modern inhabitants (who knows if the inhabitants of other worlds have strong ether like the ancients, and if their density is the normal course of nature).

Here we get even deeper into philosophical territory: what is nature? Where is the dividing line between "nature" and "not nature"? I'm not even going to get into that, but the short answer is that there are lots of different and conflicting ideas about this, among them that there is no dividing line and everything is nature.

Also, I think you're making a pretty big assumption by claiming that the Ancients were created by nature. Just as many Lalafells don't know that they were preceded by the Ancients, it's entirely possible that the Ancients don't know that they were preceded by someone else. History has a tendency to repeat itself.

Finally, I'll caution against holding up "nature" as the rationale for something being "true" or "right". There's a whole lot of stuff that is natural that the world is better off without. For example, it's natural for people to die of illness or be born with "impairments" that cause them difficulty. But I wouldn't consider these occurrences to be in any way superior due to the fact that they are natural; as someone with a disability, I'd far rather that medical science intervene and help me have a more fulfilling life, and similarly prevent me from being maimed by illness or even dying from it. Something being natural shouldn't be used as justification for its validity or sustained existence.

Knowing this in advance they could have instructed the population not to give in to desperate thoughts that would have created monsters

Unfortunately this just isn't how emotions work. Most people can't just logic themselves into not feeling fear or sadness.

So we come to a blind spot, they know the cause of the last days but they can't do anything because they can't manipulate Dynamis.

This is untrue, though: the Ancients were perfectly capable of manipulating Dynamis. Exhibit A is the fact that Hermes created Meteion, who was highly comprised of Dynamis. There's no getting around this: Meteion cannot exist if the Ancients cannot in some way manipulate Dynamis.

The shadows of the civilizations of Ultima Thule and the "Dead Ends" dungeon made us understand that perfection leads to apathy and therefore death.

Personally, my interpretation of the 3rd chapter of Dead Ends is that it's a hand-wavy cop out. If you have unlimited time and resources, you can make anything. You can change your world, you can change yourself. You could even make a 3D Sonic the Hedgehog game that's actually good! In fact, you could make millions of them! Sports, games, movies, audio - there's no limit to what you could make. You could explore the solar system, and beyond. Dead Ends refuses to grapple with any of this, instead just insisting that everyone got bored and everyone wants to die. And sure, I'm willing to imagine an alien species whose brain chemistry makes them prefer death over actually doing things. But the idea that such a contrived prospect would extrapolate to humans makes a lot of broad assumptions without challenging them in the slightest. Don't believe everything that you read!

...

Okay, now that all my counterpoints have been laid out, let's contend with the initial question: how do we save the Ancients?

I think the big question is whether you even can. For all their talk of living in a paradise, Ancient society had significant problems, and those problems eventually lead to their own downfall.

Their first problem was that their culture lacked a system to facilitate the emotional well-being of their inhabitants. Hermes felt confused by the norms and behavior he saw in his society, and it was clear that these ideas had caused him to suffer for a long time. This is an incredibly basic human problem, so to not have a system in place to address such concerns and emotional issues is careless within a purported utopia. And when most members of your society are born with powers that can literally reshape and destroy the world, investing in everyone's emotional well-being isn't just an act of decency and compassion, but a necessary preventative measure against disaster.

Their second problem was a lack of proper checks and balances. When Hermes' superior learned that he was single-handedly working on a space-faring construct — something that seemingly had never been attempted before — there was no concern, no process, no discussion of the potential ramifications. What's out in space? What could the ramifications of contact with other lifeforms be? These are questions that directly impact the well-being of every life on the planet, because you could bring back diseases or hostile invaders, etc. But no, they just let the depressed guy be the sole engineer — without any oversight or outside help — of the world's first space-faring fleet of children in thigh-high bird boots. Any decently organized society wouldn't have allowed this to happen; the Ancients were winging it, and it was only a matter of time before their lack of process resulted in disaster.

And as we saw, the Ancients had the power to destroy their entire world. At first the threat came from an army of bird girls one dude created in his spare time. Then what finally destroyed their entire society was a handful of people who disagreed with the course society was taking so strongly that they rebelled and committed genocide on their whole world. With great power comes great responsibility, and the Ancients clearly demonstrated that they did not have the responsibility to be trusted with such power. So they ended themselves.

A cautionary tale.

To be clear, what I am proposing is that if it hadn't been either of these disasters that ended the Ancients, that it would have eventually been something else. Because their society was not organized to perform an appropriate amount of due diligence, and thus problems they could have nipped in the bud were instead allowed to blossom into world-ending catastrophes. So like so many events in the real world, things seemed to be working great until it became painfully clear that they weren't. Nobody took enough time to think about the possibility of problems arising, so not only were problems not adequately mitigated, but when problems did arise they were unprepared.