Resurrecting very old post, I know...
I never bought that Lavos manipulated the planet's evolution, or created humans as they are when slaughtered. Ayla and co. were already around when Lavos fell. And yes, they were primitive, but 65-million years (I wish they hadn't written the game like that, that number is absurd) is a long time, so evolution taking place on its own during that time isn't a crazy theory. And keep in mind, had Ayla been born in 1000 or something, she probably would have been more like the people of 1000. (Some debate could be had to just how much like them, I realize, but it's at least pretty close).
It's more like Lavos is collecting the evolutionary information of the planet to form itself and carry on to... whatever purpose. (I have another post on this somewhere.)
Consider these two things:
First, if you access Lavos's inside via the Ocean Palace (probably on a plus game), the inside is the same. He's already got the humanoid form and so on, like Marle, etc., talk about. Now, this could be explained by the fact that humans exist at that point, and/or the fact that Lavos is in a way, like the Black Omen, transcending time. (One wonders if he "experiences" the 65-million years the way everything else does, or is it like a light particle that time slows down and stops for...)
Anyway.
Second, if Lavos could manipulate our DNA to control our evolution, why do it in such a way? He could just manipulate another Lavos's if he wants to produce better offspring. Why the planets of middlemen? But then, maybe he doesn't directly manipulate, but influences things some other way to kind of nudge evolution?
Hmm, I seem to be making points, but also offering potential counterpoints.
Except for the fact that humans were around before he was. So to me, Lucca's analogy of being like farm animals is more like he rounded us up, so to speak, or claimed our planet... rather than bred us to be as we are.
Although, I guess it's still possible there's a little of both in there.
So I guess I've talked myself in a bit of a circle here.