I've figured out a new backstory for Yuki as to why she can control darkness! So, this is my idea:
When Yuki was younger, around 4-5, she was just a young girl without a family, without a home, without anyone really. She was mainly just wandering all the time and hoping someone would take her in or at least be her friend. One day while she was sitting in an alley a man with a black coat showed up and decided to help out. This was before they knew about sora and the light but they saw the light and potential in the little girl. They though wouldn't think about her being a keyblade wielder. Yuki didn't quite understand who they were but she went with the man because he was the first to actually want to help her.
After taking her in, she was given a coat and welcomed there with open arms by the organization. She was practically being raised by the organization and was able to start getting the hang of the darkness with their help. That was when she was able to summon her first little kitten heartless that she was proud of but the organization didn't really like the thought of something cute, but she was just a child so she had a big imagination.
Once she was around the age of 14, when they found about sora and the bright light he had, they needed room for him so they.. got rid of Yuki like she was nothing. No one else was able to do it, but xehanort, the old man got rid of the memories of their time together in the organization.
It was only a few years when she found sora and his friends.. and she was able to get close with them but because she wasn't with the organization or remember them at all, she didn't bring sora to them which would've been helpful before.
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There we go! This is what I have for now! Yukis new backstory ^^ it would explain a lot more now. So technically she is half darkness because of that and was just thrown away like she meant nothing. She does sometimes have dreams about it but in her dreams everything is blurry because she's technically not supposed to remember and so she does wake up crying but not knowing why.