One of the rules of my characterization of Ganondorf is that he shows no mercy because he knows no one would show him any, whether in the past where he was the leader of a people feared and hated by the Hylians, or in his present where he’s gone so far that there nothing more to be but hated by his foes.
However, this rule also makes it awkward when people do show him mercy, kindness, helpfulness, companionship, or any sort of interpersonal relationship that’s not fatal opposition. He doesn’t know what to do with himself. He’s a brilliant man but so much of his mental energy is tied up with trying to gauge the intentions and motivations of those around him and assuming they are out to somehow destroy him in the end— which is part of the reason why he’s so proactive in hurting others, so he knows where he stands.
To hurt others and know his power over them, and know they hate him, is better than not knowing but feeling unsafe, not knowing if he’s in control. He knows what it’s like to be cast pariah by others and he knows how quickly those in power move to exterminate those who are hated, with none. Kill before you’re killed. Dominate everything before it has a chance to destroy you.
It’s why he keeps “kidnapping” Zelda, but underestimating Link. He sees Zelda as an immediate threat or major opposition and moves to contain her. He keeps thinking that if he controls everything, Link can never gather the elements or strength he needs to oppose him.
Ganondorf, while great, has elements of cowardice to him. This role that casts him as worthy of hatred is also how he protects himself from those who hate him, how he feels powerful over himself, others, and his place in the world. He has difficulty braving the unknown and truly carving his own path because this role gives power now, is something the world is already ready to accept him as, requires minimal risk to his self worth and identity, even if he loses.
Which is sad, because the kernel of virtue he possess is Power— the ability to change the world with his agency. He could forge a world where this fear is gone— he’s right, he has the potential to be a better King than the Hylians have, do more, be more, provide for others with the abundance of ability he has, his greatness. At some level he knows this. He wants this.
But to do it he’d have to relinquish what makes him secure in himself.
King of change, he can’t ever be benevolent while he stays the same.