The Frozen Flame is a catalyst used by Lavos. It is sent to a barren, lifeless world, albeit, it is sent to one that has the elements that COULD make up life. So billions of years ago the Frozen Flame crashes into the planet and thus jumpstarts the creation process - starting with primordial ooze. Then, when enough time has elapsed (billions of years), Lavos can show up and do what a Lavos does.
Boo, that is a nice theory but, unless I am misunderstanding you (and that is always a likely option), that would then imply that all life is a result of Lavos' influence, not just humans. I certainly got the impression from the games that the Frozen Flames influence was supposed to be limited to just humans.
Sorry, you lost me there; '2300 A.D.'?
Edit: oh, I see; what I meant was after the Zeal disaster the Earthbound became the dominant race and the Enlightened were assimilated into the collective(human) bloodline.
Yes, but what I meant is that between 65,000,000 BC and 2,300 AD there should have been a great degree of evolution taking place in the "human" genome. While there is a cultural distinction between the people in the Ioka village and the people in the Earthbound Village (or the people in the Arris Dome), there is no apparent genetic distinction (except for the apparent ability to use magic). Sans any theory, we should expect to see a significant degree of evolution between these two time periods (and indeed, between 65,000,000 and 12,000).
However, I misrepresented what you had meant, it seems, in that you are maintaining that 65,000,000 people are not humans (putting aside for the moment that Cro-Magnon's were still Homo Sapiens; same species, different sub-species, if even that). Sorry about that. Would you say that your theory, then, is similar to how I represented theory #4?
I suppose part of the disconnect might also be to what extent we see "magic" as being a significant step in evolution. That the Enlightened individuals and Earthbound are still capable of interbreeding indicates to me that magic is not a significant step; it alone cannot account for the entirety of the evolution that the
Early Human Diagram in Chrono Cross suggests. At least, I am taking the Early Human Diagram as an indication of the degree of change, even if the specific instances of that change are not accurate.
Note, the Encyclopedia gets around this by assuming that the diagram is comparing an even-earlier-version of "humans" (or human ancestors) than is seen in Chrono Trigger to modern humans. This, however, makes the diagram utterly meaningless as it no longer illustrates Lavos' influence alone, but Lavos' and nature's, making it impossible to determine what is and is not the result of Lavos' influence.
Actually that's when the dinosaurs went extinct. (source from Walking with Dinosaurs; Azala would be ashamed! 
)
That too. More than one thing happens at a time, however. Even in the real world, mammals were around when the dinosaurs went extinct. To illustrate, the Class Mamalia developed between the Permian Period and the Jurassic Period (thus, very roughly, between 275,000,000 and 175,000,000). So, as mentioned, if I am remembering my anthropology course correctly, the Order Primate was developing during 65,000,000. That is significant as this is too early for even Australopithecines (indeed, the split between old world and new world monkeys wouldn't have occurred yet!). If we compare real world evolution to Chronovolution (as the Early Human Diagram seems to imply that we should), Lavos' influence on humanity should be on par with changing proto-primates into Homo Sapien Sapiens. Yet the games also indicate that Ayla's people, who are at the best a subspecies (Homo Sapien Iokien?), were already present at the time period (thus indicating that real world evolution shouldn't be applied).
However, looking over the script again, perhaps the entire discussion of "Evolution in the Series" is a misguided one. To quote the Dragonian Record from CC (emphasis added):
However, the timid '"apes"'
who had lived hidden in
the forests...
...came into contact with
the crimsom flame
that fell from the sky,
and evolved into '"humans."'
Or perhaps it was
not '"evolution,"'
but '"transformation."'
In this way, humans
increased in number
and filled the earth...
The fearsome '"progeny of Lavos"'
who, like their progenitor,
began to devour our mother planet.
Humans changed between 65,000,000. Perhaps, then, the implication is that if humans were the dominate species on the planet and if Lavos never fell, they'd have "evolved" (or changed) more along the lines of the Reptites, as beings close to the planet (which then implies that there might be a Apeopolis in an alternate dimension with a plasma lifeform called the Gorilla God).
Certainly, a hallmark of the Reptites and Mystics (two species presumably not tainted by Lavos) is their diversity. They aren't species that act independently but in tandem with other creatures (Imps, Gargoyles, Naga-Ette, bats, and all sorts of "monsters" on one hand and Reptites, Winged Apes, Volcanos, etc on the other). Indeed, we see the early humans possibly starting this behavior (through there use of the Dactyls). Even Zeal, having recently switched to Lavos' power, interacted with the Dreamspecies and the Nu, whereas after that point Humans are a solitary species, not interacting willingly with the other lifeforms of the planet.
And to quote one of the Chronopolis Ghosts:
Beginning with a cerebral
neocortex, which only
exists in higher mammals...
The anthropod brain enlarged
at an accelerating pace until it
became the human brain we know.
Could the reason for the
abnormal development of the
human brain be the biological
contamination caused by Lavos?
This could be taken as an indication that the human brain's size is abnormal (and it could also be taken as an indication that the Reptites are either mammals or do not have a neocortex), or it could be taken as an indication that the size is proper but the actual function of the various parts of the brain are flawed (the PVN, or the brain stem, or the hemispheres, etc). The difference intellectually between Ayla and Lucca, then, might not be in the nature of the size or potential of their brains but rather how they are hardwired.
And finally:
In the eyes of the Dragons,
we humans are the foes...
A brain that has developed abnormally
to 3 times the original size in the
span of 3 million years...
We humans have evolved at an
enormous rate because of our
contact with Lavos's flame...
In a sense, mankind is Lavos's offspring...
We humans are extraneous to this planet...
This last quote, then, is the troubling one that implies we should apply real world evolution to the series. I would propose, then, that it might be best to assume that this is the result of dragonian propaganda and the individual's own misconceptions and errors.
This isn't to say that we can't apply some degree of evolution to humans, but rather real world evolution doesn't fit and the stated period of that evolution are nonsensical so they can be discarded as sources of valid criticism.
We can still have that humans, under Lavos' influence, developed into Zealians (with the Earthbound being influenced by not to the same extent), which then re-converged into modern humans (a fine and commendable interpretation, if real-world evolution is not held to). Or even that humans evolved into Mystics as well (I do like that theory).
And even in discarding the restrictions of real world evolution, we are still conforming to many instances of "evolution" as presented in the game.
