At the end, there are two reveals. One: Celestial Maidens need human males to reproduce. Leaving their Celestial Robe (or "Mana") for a male to find and then marrying him is the usual procedure, and in fact they are apparently quite jealous of humans for whom getting kids is so easy. OK, fine. Two: Tooya was created by Ceres' own power, by her own Mana. And he made Aya/Ceres pregnant. So.... what exactly do they need humans for again?
Ceres was a full-blooded Maiden, but Aya was one of her (mostly) human descendants Ceres was haunting. Tooya, while male, is essentially a full-blooded Maiden as well. Thus, his making a baby with Aya amounts to the same kind of cross-breeding with humans that Ceres did with her husband, just with the sexes reversed.
Don't celestial maidens cross-breed with humans to create genetically superior offspring? The Mana is a part of Ceres's body (recall that she is literally incomplete without it), so it might have the same or similar genetic material as she does. That said, what bugs me is how no one else seems to be bothered by the idea that Aya's pregnancy has some serious inbreeding/self-fertilisation thing going on.
As noted, though Ceres was time-sharing Aya's body with her, the body was Aya's. The anime doesn't mention how many centuries back this family goes, but presumably a whole lot of generations stand between Aya and her ancestor Ceres, to whom Tooya is presumably a genetic twin. With all the new genetic material introduced to the family line with each generation (unless a lot of Kissing Cousins are involved), any generations that preceded your great-grandparents are no more closely more related to you genetically than just about anyone from your ethnicity. Tooya may (by whatever quirk of Maiden genetics allows for opposite-sex clones) be genetically identical to Ceres, but the only thing linking him to Aya genetically would be her very diluted Maiden factor. One might still think there's something intuitively creepy in sexual relations between a girl and a being genetically identical to her ancestor, but they're not close relatives by any scientific standard.
It's mentioned early on in the manga that the Mikage family have been marrying cousins together for hundreds of years.
Also, if I'm reading events correctly, it took the hagoromo something like 5000 years of sitting in the ocean to evolve into Touya.
Watase also mentioned in a free-talk in Volume 14 that Touya was a genetic amalgam of all the men Ceres has been with. So at least some "experience" on Ceres part was apparently required for Touya's creation.
How does the C-Project actually work? Okay, I get that Kagami poisoned Japan's water supply with a drug that makes Ceres's female descendants ascend to their Maiden forms, hence the sudden increase in Maiden characters. But then how did Kagami manage to get all the Maidens he placed in his secret underground society to consent to the experiment and happily become his baby factories? When Aya turns herself over after the Chidori incident, he explains all of women involved with the project gave their consent. Uh, how? We're shown he conveniently owns a brainwashing machine that he uses to awaken Aki's Ancestor alter-ego and attempt to suppress Aya's memories so she's in 24/7 Ceres Mode, so are we meant to assume he also used it to make all of the captured Maidens docile and was outright lying when he said they willingly joined the program? I'm not saying he's not a big enough bastard to pull it off that way, but if that's how it works, why didn't Watase just up and state this instead of leaving it all ambiguous? Or does his organization use some Handmaid's Tale-esque mass psychological conditioning on the mothers-to-be? Or does he only take in Broken Birds like Miori, who have already grown cynical toward humanity and have pre-existing reasons to think the C-Project is a good alternative? Is disgust in the human race just a natural characteristic for awakened Maiden descendants, and Chidori and Shuro were random exceptions to the rule? It just seems like a huge element of the plot that was never explained at all.
Stress does seem to be a key part of a celestial maiden's awakening, so the most powerful being Broken Birds is hardly unrealistic. Probably is some low-key psychological manipulation going on as well, bordering on More Than Mind Control.
At least some of them may well have volunteered, under the impression that they would breed a higher form of humanity, make the world a better place, or the like. People in real life have voluntarily gone through some squicky experiments For Science!.
Looking more closely, every descendant does seem predisposed to have a somewhat low opinion of the human race, it's just that the lucky ones have enough healthy interaction with sane people for them to change their minds. Considering the large number of explosions that occur when they ascend, people were probably rather scared of the "sole survivors" of the "accidents" and eager to be rid of them. Thus the Mikage probably didn't have much trouble putting them through standard cult indoctrination; separate them from positive outside influences and repeatedly show evidence of the world's evil, place them in an environment where all their needs and desires are fulfilled, tell them they are "different" and "special" and and prove the latter by showing them how to use their newfound superpowers... "I'm descended from ancient divine beings, I've just become divine myself, and you want to protect me from stupid evil people while I have divine children who will inherit the world? Sounds great!"
Toya is a human body, manifested out of Ceres' mana. The mana is said to be a part of the celestial maiden. And he got Aya pregnant... considering Aya is said to be the closest to Ceres in terms of the same genetics out of the entire Mikage clan. So... does this mean that she technically got pregnant by herself? How would that even work in terms of genetics, without resulting in horrible genetic mutations, given the close proximity of the DNA being practically the same?
A Wizard Did It. The mana is essentially a piece of Organic Technology that enables a Tennyo to gauge the suitability of a male at the beginning of her lifespan and change into a form capable of returning "home" at her end. Except in Ceres' case, it was thrown into the ocean and spent the next five millennia interacting with random lifeforms according to a vague "find good genes" protocol, of which Tooya was the ultimate result - five thousand years of searching for choice genetics; superhumanly strong, fast, resistant to damage and capable of extensive self-repair. Tooya is not at all related to Aya, he's the epitome of what a Tennyo is supposed to seek out.