Bonney is:
-A giant eater
-A character with tons of mood swings
-Obsessed with revenge and getting back at people who wronged her and her family
-Has pink hair
-Is a child, as shown by her being in child form after leaving the ocean (why would she be trying to sail a ship as a child? Her being a child in this situation only makes sense if she reverted to her original form due to sea water)
-Is obsessed with the parental figure who was stolen from her, but, the way they were stolen from her is not what she originally believed
-Has the same heart-shaped lipstick as Big Mom
It's pretty clear at this point to me that Bonney is a clone of Big Mom.
This whole arc revolves around cloning, and this would make Bonney a direct parallel to Yamato, with Yamato being Kaido's child who was often starved and enslaved by her father, while Bonney's a huge eater that is trying to save her enslaved father.
This is why Vegapunk has acted the way he has: Vegapunk views Bonney as his child, too, since he created her.
The question would be then, "How did Kuma and Bonney meet?" If Dragon and Vegapunk were close, maybe Kuma was more willing to work with Vegapunk from the start than we assumed, and had known him closely? Maybe Vegapunk had Kuma protect Bonney from the WG and "kidnap" her? Lot's of places Oda can take this.