Elidibus was Zodiark and Zodiark was Elidibus. And Elidibus had done quite a lot of evil sh**t.
The creature we killed in Lamentorum was basically a pilotless entity without him. Primals are defined by their primary creator wishes, think how Titan was like a child in distress on his botched summoning.
As for Hydealin, people don't realize the ancients would sacrifice life ( which includes intelligent life, like you know, FF14s races) to bring back the Amarautians.
Ignoring the fact that they did not have the right to do such a despicable thing, the unsundered ancients woud be a) unableto stop Meteion due to their higher Aether and inability to use Dynamis b) even if they stopped Meteion, they would still die like all the other civilization Meteion met, so they would commit the massive genocide for no reason!
Amaraut was done for.
So knowing this, she "cheated" this destiny by sundering everyone into our lesser forms, which would struggle forever, but yet fight to survive and build great things nevertheless. She is not happy about it, but it was the best solution, from her POV.
And before someone says this is not hinted anywhere, this is literally the core meaning of "Aswer's" Lyrics. They might not have nailed down every detail, but the general concept/themes were there from day 1:
Now open your eyes while our plight is repeated
Still deaf to our cries, lost in hope we lie defeated
Our souls have been torn, and our bodies forsaken
Bearing sins of the past, for our future is taken
...
Tell us why, given Life, we are meant to die, helpless in our cries?
Thy Life is a riddle, to bear rapture and sorrow
To listen, to suffer, to entrust unto tomorrow
In one fleeting moment, from the Land doth life flow
Yet in one fleeting moment, for anew it doth grow
In the same fleeting moment thou must live, die and know