Humans didn't come from the Cetra; the Cetra came to the planet and were there when whatever humans were evolved into humans. It was then that the human race had an explosion of banging and overpopulated, and the Cetra fell almost completely out of existence. The Cetra were the miads of the planet basically in their time on "Earth". Whenever the planet was harmed, they nurtured it back to health. Think of the time when Earth was a mass of molten rock; think that everytime a stray meteor hit Earth, a bunch of people would run up and pour peroxide on the wound. That's basically what the Cetra did. They could also open up "vents" for the lifestream to pool out, allowing it greater access to the planet to heal it if it were harmed.
Or, the Humans and Cetra could be one and the same? Maybe the 'Cetra' was really just one particular culture/civilization that was more advanced at the time (more well-versed in magic and the workings of the lifestream) and were therefore the most potent threat to Jenova at the time? Would explain why Jenova attacked the Cetra first and foremost instead of wiping out all life and then attacking the Cetra.
Maybe the Cetra were slightly genetically different in terms of ESP (kinda like how some folks across the world have darker skin, or different-shaped eyes) and this enabled them to communicate more readily with the planet, and this ESP-enhanced ability is seldom found in the majority of the rest of humanity, leaving the remaining Cetra -- like Aerith -- virtually the only ones capable of communicating with the planet directly? Thus making them the ideal candidates for working with and defending the planet, reacting quickly to the planets' needs?
This means, of course, that far in the future, humans as a race will get more and more ESP-oriented abilities as they evolve. Essentially, turning into what is recognized as the Cetra, for their ESP abilities allow them to communicate with the planet, and their deeper knowledge of metaphysics allow them to easily harness magic, the way the Cetra were fabled to.
This makes more sense to me, honestly. Humans suddenly overpopulating and pushing the Cetra out was merely Sephiroth's delusion. In truth, the Cetra were pretty much annihilated in the war with Jenova, and the remaining Cetra had no home, no civilization, and essentially no people to return to. Likely, they just did as Aerith's mother had done, and gone to live amongst the less advanced humans, melting into that genetic pool instead.
But that's just my spitball theory!
