You could look at it as a non-literal meaning of the word "evolution"...so many people use it wrong these days anyways...The Sun Stone was an item of great power that allowed them to do great things. I could see them thinking of that as a kind of 'evolution'. There's a lot of open history there we just plain don't know about...
Very good point. One of the annoying things about "evolution" is that it changes meaning if one capitalizes it or not. Capital E "Evolution" requires genetic change of one species to another, but lower case e "evolution" can just mean change (as in one species changing into another, or the same species "changing" by developing culture, magic, etc, or it could mean the extraction of a root from a quantity, in mathematics).
The problem is, however, that the Earthbound seem to lack the genetic trait, not just the knowledge, of how to use magic. If magic is merely knowledge, then there would be absolutely nothing separating a year old Earthbound child from a year old Enlightened Child. Indeed, if it were knowledge alone then Robo should be able to learn magic easily enough. Indeed, if magic is knowledge then any individual should be able to learn to use any time of magic. Likewise Ayla, despite living prior to the development of magic, should still be able to use it (she lived before the development of Time Travel too, but that doesn't stop her from using that knowledge). Rather, magic seems to be a combination of genetic ability and knowledge (sort of like the World-Walking ability/W* heterozygote gene of the Merchant Princes series, by Charles Stross).
It is curious that over the course of 65,000,000 years the Reptites evolved into a different species (the Dragonians) but humans did not. This establishes, if nothing else does, the expectation that Humans should not exist both in 65,000,000 and 2300 A.D as a single, unchanged species.
So, give that, if I might try to methodoligically review things.
1) Humans should have evolved into a different species over 65,000,000 (as illustrated by the change of Reptites to Dragonians over that time period).
2) Evolution need not necessitate physical charge; the development of magic required the development of knowledge of how to use it.
3) However, magic ability is still in the realm of one's genes (as illustrated by Ayla and Robo being unable to use it, as well as the separation of the Enlightened Ones and the Earthbound).
I just realized that we might actually see the different species that humans were to evolve into; the Mystics.
From that, if I may extrapolate wildly (and I do mean wildly); humans did evolve and separate into various species in the 65,000,000 years between when we first see Ayla and when Chronopolis conducted its research. However, the species evolved into the Mystics (thus solving why there is no significant genetic change over such a long period of time). Even among humans we see what might have eventually led to separate species; the Enlightened Ones and the Earthbound. To note, evolution doesn't necessitate that the previous species be replaced; Coelacanths, for example, were note replaced, whole hog, by more "evolved" species.
Thus the Frozen Flame might be said to have three possible influences on Evolution; it could speed it up (but we don't see actual evidence of this in the game, only the indications from Chronopolis), or it may have no effect whatsoever on evolution, or it may slow it down (as humans remain largely unchanged over the course of 65 million years in game). This later possibility seems to conform to the "physical" evidence of the game and only contradicts Chronopolis.
This also then allows for the lines in Chrono Trigger about a "strange red rock" to still mean Dreamstone (which I believe was the original intent, rather than the later retconning it as more analogous to the Frozen Flame). To quote both the NA and ReTranslation versions of the book:
It all began aeons ago, when man's ancestors picked up a shard of a strange red rock...
Its power, which was beyond human comprehension, cultivated dreams...
In turn, love and hate were born...
Only time will see how it all ends.
Tens of millions of years ago, the ancestors of humans happened to take a fragment of a mysterious red rock in hand...
Everything started from there.
A power that surpassed human knowledge gave rise to dreams and gave birth to love and hate...
What manner of ending will that see...?
Perhaps only time knows the answer.
If the above is not total bunk, this would then help develop the dichotomy displayed in the series (Human/Reptite, Lavos/Entity, and Frozen Flame/Dreamstone). The biggest argument against Dreamstone causing human evolution is the argument that Dreamstone existed in human hands long before Zeal. While true, that doesn't indicate that evolution didn't occur. Human intelligence existed in 65,000,000 and thus may have already been the result of dreamstone.
Second to Last Note: Boo, there actually is some evidence for your theory that humans in 65000000 were transported there from the future; Kino came from the Mystic Mts, possibly through a gate. And Leah, likewise, traveled to the future and stayed there for an extended period of time. It is quite possible that Kino was from the future, and if Leah could travel to and live in the future, a future individual could travel to and live in the past.
Final note: While the Sun Stone may have also had some influence on this “change,” such an influence isn’t even hinted at.
