I think the Kikwi become the Kokiri and Bucha is the Great Deku Tree. All of this is speculation, but here is my idea.
After the Hylians move back down to Hyrule, Bucha, who had taken the same form as the Kikwi in the early ages of Hyrule, "plants himself" as a Deku seed. Then their corner of the Faron Woods becomes isolated as the Lost Woods. The rest of the Kikwi live the same way for an age until the events leading up to Ocarina of Time. Link's mother brings him to the Lost Woods, and the Deku Tree (Bucha) agrees to raise him. He causes the Kikwi to change into the form of Human children so that Link will grow up in a familiar environment. While Link is a baby, the Kokiri build their homes and develop their culture, so that by the time Link is older, he has a community in which to live. A hundred years later, with the coming of the Great Flood, the new Deku Tree causes the Kokiri to transform again into the Koroks so that they can fly around and replant the forest.
Throughout everything, they remain sentient plant-spirits, but in Ocarina of Time they take on the form of Human children for Link's sake.