Perhaps I should explain my reasoning.
First off, let's look back at OoT. In the Sacred Forest Meadow atop the Moblin-infested maze, there is a Gossip Stone that reads (when wearing the Mask of Truth) "It is said that Kaepora Gaebora is an incarnation of an ancient sage". He is an owl, but none of the Sages in the game are owls. So the question is: Which Sage? The answer: Obviously the Sage of Light, simply because Rauru's physical body is long dead and only exists in the Sacred Realm. Besides, the two resemble eachother quite closely, do they not?
Now let's refer back to WW. We have the King of Hyrule and the King of Red Lions. The two resemble eachother closely, and are obviously incarnations of eachother. But, one is a boat, and the other is human. How can this be?
It is the same for the Zora/Medli scenario. An incarnation in Zelda does not have to include two members of the same tribe or race. This is highly mistaken by the fact that one's incarnation may have descended from the original being, but this has not been proven. Also, in Bhuddist and Hindu mythology, reincarnation is not believed to work this way either. Because of Karma, one's spirit may be reincarnated into a dog or bird or insect. And looking at incarnations from the Zelda series, we know the same rule applies.
Kaepora Gaebora(Owl) = Rauru(Human)
King of Red Lions(Boat) = King of Hyrule(Human)
Medli(Rito) = Sage of Wind(Zora)
But do we infer from this that humans evolved into owls or boats? Of course not.