Etheirys was always rich in aether and would have had even more of it to work with before the Sundering with the benefit of an even stronger and longer lasting Zodiark serving as a shield against the return of the Final Days.

Given that Venat, seemingly alone and in a Sundered state herself, was able to create not only a huge prison for Zodiark but a giant spaceship and an entire race of useful servants in which to run it...one can only wonder what the entire might and minds of the Ancients working together might have accomplished had Venat simply sat down and told them everything that she knew before the Final Days even manifested.

Much as how wiping out the Garleans because they couldn't easily manipulate aether wasn't acceptable in the eyes of many, so too is it not acceptable to wipe out the Ancients just because they supposedly could not manipulate dynamis easily.