Thinking that perhaps Mr. Jonathan Crow was created in the image of someone via Kanna's desire to see that person again. Is not that original person, but is instead a reflection of Kanna's perception of a Jonathan who is no longer of this world.
As such, Mr. Crow has turned out different than expected. And as he has grown familiar with his existence, he has taken on his own personhood, separate from the person that his features were originally based on.
Though it also sort of means his old existence that he remembers, his "old life"...isn't real, at least for him.
But I think Kanna loves him even more, because its her fault that he exists...even if its not the person she was originally missing.
Jonathan Crow is still someone who deserves to be cared for, loved, simply because he is who he is.