User blog comment:Admiral Sugar/Thoughts on Devil Fruits/@comment-1405658-20140221025302

While it doesn't answer most of your questions (it may raise more), I think they came from, and are deeply intertwined with the Ancient Kingdom of the Void Century, Sea Kings, and even The Will Of D. We know Ancient Kingdom had some connection to the Sea Kings (Ancient Weapon "Poseidon", maybe even those curious archway carvings on the way up Reverse Mountain).

Sea Kings and Devil Fruit users have a common "weakness", the same frequency of seastone, which affects their ability to sense ships (but can see them), while severely affecting users.

Sea Kings and Will of D may have some connection, in that both Gol D. Roger and Luffy could hear Sea Kings (the "voice of all things"?).

Will of D might be similar to Devil Fruits in their nature. "Inheirited will" is mentioned, Luffy hearing the same voices Roger did with the Sea Kings, and Roger saying to Rayleigh that he won't die. Inheirited Will (and hearing the "voice of all things") may be linked in that skill is what Luffy inheirited, as a reincarnation of Roger. His hat passed to Luffy, he had similar events happen. His "ability" might have been reborn into another person, much like a Devil Fruit power passes to a new fruit. It may or may not be linked to the Conquerer's Haki, too.

Ancient Kingdom and Will of D might be linked, from Whitebeard's flashback with Roger, the story began: "Long ago and far away...". I wouldn't be shocked if the "D" are all carrying the will of dead Ancient Kingdom citizens. Nobody so far was sure about the initial (like Saul) or why that was the name, maybe it's similar to how a fruit gets all twisty when a devil fruit reincarnates?

Sorry for the wall of text, but it all leads to this: Devil Fruits may have been phase 1 in the experiment of the Ancient Kingdom to attain some kind of immortality. They might have appeared during/after the attack by the alliance as a way to leave something behind, like the poneglyphs. The "D" are probably the successful experiment, where the "will" passes to another person, and the Devil Fruit are for a similar purpose, either as a prototype (affecting "lineage factor", likely DNA), a means to stir chaos (and give an individual the literal power to shake the world), or to arm the inheiritors if need be. I don't know if it ties into "will", but we'll see when Ace's fruit is consumed, testing the mention of someone else picking up for him.