While I don't think Vegapunk may be completely right in his theory, I think he's going to be shown to be on the right path in regards to Devil Fruits.
There is a piece missing, but I don't think it involves the souls of others. At least, I don't think they were imprisoned in trees. If we get more info that implies DFs are a form of imprisonment or control, I think I would start leaning towards that path, but at this moment, it seems like DFs may have been another way to pass down one's will, similar to the Will of D. I will say, the whole Soul thing would make sense as to how DFs manifest elsewhere in the world, though that would imply that Paramecia and Logia have wills of their own as well and, so far, it only seems like Zoans have that trait. That would also open up another can of worms on how Brook's Fruit and Big Mom's Fruit could potential function.
Personally, I'm thinking a piece of technology allowed people to tweak existing Lineage Factors, thus the various wacky abilities, and then distill them and turn them to Fruits. Science brought those desires into existence, which would allow Vegapunk's romantic theory to be true in a sense, while also being incorrect.
I think Lineage Factors are just going to be revealed to be much more powerful than people assume and the essence they possess goes deeper than DNA. So...thinking about it now, just the whole Soul idea wrapped in a different package.
We also still got aliens mixed in too, so maybe they play a role somewhere down the line.
