Doesn't Hako's ability to manipulate her plushie seem similar to the Puppet Master Technique? Her hands are hidden, so this probably be the most probable thing.
I hope this doesn't count as fanfiction, but would it be interesting to see it be a soul sealed into the plushie? Like someone that wanted to protect had sealed their self into it. As a way to protect Kuroi as she continues her life as a shinobi.
Instead of being the unconfirmed child of Kakashi, why not say he is someone who idolizes him. Someone who wants to emulate him, and become a shinobi that could be compared to the Sixth Hokage.