But we must remember, in light of the "Could it be..." that this is just a hypothesis that is made. As I have said before, this referral to humans being "Progeny of Lavos" is unique to Chrono Cross, and as such I think is Dragon Propaganda. Certainly the human brain is more advanced than are most animals, and the murals in Fort Dragonia would profess that this is as a result of Lavos' intervention. This, however, cannot be when looking at the wider Chrono universe. As prehistoric as Ayla is, she is self conscious and has what might be termed an evolved mind. Keeping this in mind such tampering by Lavos is impossible, and the murals must be nothing more than Dragon hate literature for the race that wiped them out (and this hatred for those "apes" we see all too clearly from Azala in CT). It comes down to either trusting to the Dragon's words, or what is shown and seen by Crono in Chrono Trigger. I side with the latter.
That being said, while the Frozen Flame, ie. Lavos, is not responsible for human evolution, then it might be said that the culprit could indeed be the dreamstone itself. I am willing to guess that this was also responsible for the Reptite evolution, but that is an entirely different matter, and likely occured centuries before. All along the Dragons say that the earth despises humans...and yet it is they, not the Reptites that save it. It was not they, but the Reptites, that doomed it with the summoning of Lavos. Perhaps the earth saw all too well that the Reptites would die; perhaps humans were the "plan B" as it were. The Dreamstone is certainly a magical thing that is of this earth. That being said if it is the culprit for both Reptite and human rise, both races rose according to the will of the "entity". Though I would like to imagine this entity as God, or perhaps fate, I am certain that it is meant to be the planet. This would cast much doubt on the incessant dragon/reptite claims that humans are something of a plague or misfit to the planet. They are different in skill, certainly, and further removed from things that grow. But maybe it is through this virture that the entity knew victory against Lavos could be accomplished, and so brought forth a new, younger race to surplant the older. Naturally the Reptites wouldn't take kindly to this, and speak evil of humanity.
I would say that the Reptites were fairer seeming, more beautiful and in tune with the earth and such, but in the end had a flaw: they could not stop Lavos. I wager that in their home dimension Lavos was never stopped.
It is an interesting thing, I believe. And in a strange parallel, might draw unadvertant comparisons with Tolkien, perhaps. The Reptites are the older race, as are the Elves. The humans are the younger born, and are destined to surplant the older. But whereas in Tolkien the Elves take this as how things must be, the Reptites fight what is fated, and are destroyed. Also in the Chrono universe it says numerous times how frail humans are; well, in Tolkien men, compared to elves, are sickly and weak seeming, though among the ranks of men there are a few that stand mighty even among the Elven Lords, and do things that even they could not do. This and the fact that Zeal bears greater resemblance to Numenor than anything else (even Atalantis). But that is a different topic, I should think.
I know this has digressed significanly from the main topic, but it all stems from the dreamstone. It is through the dreamstone, I think, that both races rose. As it says in Zeal, it gives birth to hopes and dream; this is likely what it is, the magic of hopes and dreams, of feeling and emotion. And so it can be shaped by those that hold it, it not being so much a physical thing but merely a home to the spirit, even as the body is merely the home to the spirit. Perhaps a part of the earth, even as the Frozen Flame is part of Lavos. And this theory would make the humans no strangers, but the successors to the Dragons, and in a very real sense the heroes; they who succeeded in skill where the Dragons failed of their promise.