I don't really see it that way, myself. It feels like you're being wayyyyy too harsh on Hydaelyn's creators.
For one thing, the Amaurotines were portrayed as a genuinely wise people. They most likely the selected the sacrifices of Zodiark in such a way that society could continue as best it could, and therefore the costs to each sector were likely even. Zodiark was also made in somewhat of a panicked state to stop the calamity, which means that if there were glaring flaws in making either of them, they were likely first made in Zodiark.
Conversely, Hydaelyn was planned out in secret, and had a relatively longer time to be planned out. Her core concept may be relatively simple, but that didn't mean it wasn't clear.
Also, consider the name of their hideout: Anamnesis Anyder. From a r/ffxiv reddit post:
I don't think it's inappropriate to translate this as 'place of reflection' or 'place of memory'. It seems to be where they stored their concept crystals. So it's not like this is a place run by idiots or anything like that.