Zodiark seems to often be framed negatively by the game's writers, despite — if I understand the lore correctly — never having done anything negative.
The Convocation made Zodiark to save the planet from The Final Days, and while this did not tackle the root of the problem, he did succeed in protecting the planet. It took a sacrifice of Ancient lives to create him, but they did so willingly.
However, the planet had been damaged in such a way that it wasn't flourishing the way it used to, so a willing group of Ancients sacrificed themselves so that their aether could fuel Zodiark in solving that problem. And he did. Cool. So far, Zodiark is just doing good things and the folks fueling him are willingly making personal sacrifices to help their planet. Admirable.
Now here's where it gets iffy. A seeming majority of the Ancients wanted their fellow Ancients who had been previously sacrificed to return to life. To fuel this, the plan was to offer Zodiark some of the "life" (I don't believe it is ever specified what form this life took, whether it was plants, animals, sentient non-Ancients, etc) that had developed. The implication is that this 3rd wave of sacrifices would differ from the previous ones in that they would quite understandably not be consenting to this. So this comes across as selfish, as sacrificing the well-being of an out-group to satisfy the needs of your in-group. Not cool.
However, here's the thing: from what we're told, it sounds like the Ancients are the ones who wanted this sacrifice to happen. And while it's implied that Zodiark would have done it (as he was a creation that was presumably subservient to the desires of those who had created him), he didn't instigate the plan and he never even did it.
Meanwhile, Hydaelyn most definitely committed genocide. Wiped out an entire race of people and their culture. And let's be fair: she did this to prevent a great harm from occurring. But surely there was another way to prevent that besides literal genocide. (Especially since in sundering everything, she sundered not only the aggressors, but also their intended victims.)
In Endwalker, Urianger has a very thoughtful monologue that contains this quote:
"No effort did I make to see out alternatives. Ones that would not demand such terrible costs. That resignation weigheth heavy on my mind"
When I think about Hydaelyn, I think about that quote.
I don't think any of this is as simple as "X is good, Y is bad", but I do feel like the game frames Zodiark far too negatively for an entity that saved the planet and then almost did something bad, while Hydaelyn is framed far too positively and uncritically for an entity whose solution to the problem of mass-murder was a world-wide genocide.