I have a theory as to why Zero Two looked human.
So she was originally a red Klaxosaur-human hybrid and at some point, they had her begin piloting Strelitzia. APE eventually realized that when she piloted with human stamens, she consumed them, and the more she consumed, the more human she appeared.
Knowing her desire to be human, they then weaponized her obsession by telling her that the more klaxosaurs she killed, the more human she would become. In truth, it was the human pilots she was consuming that made her look more human.
I think this is why she doesn’t pilot with the Nines because APE needed human fodder to maintain the lie and keep their most powerful weapon fighting for them.
When Zero Two met Hiro, she was moved by the way he treated her. Unlike everyone else, he didn’t see her as a monster, despite her reputation. Though she didn’t consciously remember him, Hiro reminded her of her Darling because, of course, he was her Darling.
When APE learned that 016 was able to survive her and that she liked piloting with him, I think thats when they realized they were already close enough in their plans and decided to get her to the Grand Crevas. They didnt need to keep her human forever, they just needed her to breach the Crevas.
However, because his contaminated DNA allowed him to survive her, he wasn’t providing enough of the human DNA she needed to maintain her human form. As a result, she began to regress. This is also why she grew increasingly impatient and desperate to kill more klaxosaurs.
She eventually lost faith that Hiro was her Darling. Frustrated and impatient, she decided she was done waiting and would take everything he had left to offer, so she tries to consume him entirely. (And this is how he saw into her mind.) But then she realizes the person she was using really is her Darling.
So why did Zero Two start looking more human again later? Her treatments at the Garden were likely supplements designed to compensate for the lack of pilots she was consuming. APE probably sacrificed stored parasites from cryo to maintain the effect.
In the end, Zero Two believed that killing klaxosaurs was what made her human. The truth was that consuming human stamens was what made her human, and APE weaponized that belief to control their greatest weapon.
This is my theory anyways, and maybe its not solid but I enjoyed the idea atleast.