Well, so as to not let the thread die for want of effort on my part, I suppose I'll see about addressing some of the theories and weed a few out (mind, final conclusions however would really need to wait until the respective proponents extrapolate the original theories.
So, Theory #1: The humans in 65,000,000 BC, as seen in Chrono Trigger, are really from the future. Simply put, Humans are so evolved in that time period because evolution already took place. This does get around the problem of the seemingly different models of evolution displayed in CT and CC. It is not without some circumstantial in-game evidence either, particularly in the Mystic Mts., at which Kino was apparently found by the village chief (curiously, it is indicated that Ayla was probably chief at around 5 yrs old, 10 at best). As that is where Chrono and Co appear, it might be that Kino is like Leah, a time orphan.
While a very interesting theory, it doesn't have much going for it. It requires a fairly large supposition (that humans traveled back in time to found humanity) and doesn't deliver on equally significant justification. With more proof, I think we have to discard this one for now.
Theory #2 is that the Sun Stone evolved humans in some fashion, thus replacing the Frozen Flame as the agent of evolutionary change. This is supported by the fact that the stone radiates a significant degree of power (and that power could probably cause genetic mutation), however the Sun Stone is never presented as anything but a power source (and importantly, a power source that is not present in 65,000,000). Thus this theory necessitates that attributes be applied to the stone that aren't indicated in the games and that the stone be present in a time period where it appears to be absent. Without further extrapolation, I think we have to discard this theory as well.
Theory #3 specifically addresses a single problem; IF the Frozen Flame is part of Lavos, and IF humans are almost totally "evolved" when Lavos lands, then the Frozen Flame must have gotten to earth before lavos (hence, it was sent into the past and evolved humans then). Even assuming that this were a possible explanation, it doesn't address another problem that is equally critical and makes this one slightly nonsensical; humans didn't evolve from 65,000,000 to 12000. Even if the Frozen Flame traveled into the past, there should have still been some form change during those many years. Indeed, Chronopolis humans should be even more unlike the image of -pre-frozen flame "humans" than the 65,000,000 humans are.
Theory #4 is more satisfying in that evolution does occur during this period; the Enlightened Ones evolve. However, this still indicates a very small change (magic power) and it doesn't address why the Earthbound did not evolve at all (thus returning to the problem of the Chronopolis scientists not conforming their theories to the reality that we the players see).
Theory #5 only addresses the magnitude of Theory #4; humans evolved into Mystics and the ones remaining as humans were actually comparatively un-evolved; therefore the Chronopolis scientists were assuming a degree of evolution happened that didn't actually happen to the given subject (but this should have been revealed by studying human DNA). This theory really only addresses part of #4 that was weak but it really has the same weaknesses.
And finally Theory #6 has the problem of assuming that Chronopolis scientists were fundamentally wrong; the Frozen Flame didn't help evolution, it prevented it. Unfortunately this is not very satisfying as it requires the source to be considered wrong and the theory to be considered correct. However, humans would still be considered evolutionarily aberrant like gets mentioned in Chrono Cross.
Unfortunately, I don't think we can get away from the fact that the Chronopolis scientists must have been fundamentally wrong in some way; the time scale of change must be off, or the degree of change, or some such.
