Schala (Appearance Changes)
Why did Schala's hair turn blonde in Chrono Cross? Note that her eye color also changed from green to blue, leaving this as a possible plot inconsistency.
Schala Hair Dye
While the royal family of Zeal all had naturally blue hair, Schala did not. Instead of allowing her to be ridiculed, the royal family of Zeal simply had her hair dyed blue to match the others. This dye wore off during her internment inside the Time Devourer.
Bleach Effect / Genetic Alteration
The nature of the environment of the Darkness Beyond Time and the Time Devourer caused her hair to become chemically bleached. However, this would mean her scalp would suffer from the same effects, which is problematic. Also, why would Kid have blonde hair?
Another tenet of this theory holds that since Lavos was able to recombine DNA, the Time Devourer made some changes to Schala when she unified with it. This might have changed her hair blonde and her eyes blue, which means any copy of her (Kid or Harle) would keep the effects.
Epigenetics is a relatively new science that deals with modifications of cellular DNA expression that don't actually change one's original DNA at all. These epigenetic changes are passed on in cell division, as well as the unaltered, original genetic code.
Your epigenetic code is a 'second DNA'. It sits right on top of your original DNA, and unlike the original, it can and will change during your lifetime depending on environmental situations. In recent studies, identical twins of all ages and walks of life have had their epigenome compared with one another. The older the twins are, the less epigenetic similarities they have, until they are extremely different in old age. These changes occur because of environmental factors--smog and pollution, smoking, food, chemicals we are exposed to, even how we behave and act towards one another, etc.
Shifting back to Schala and Kid, epigenetics would be a huge reason why Kid and Schala look (and perhaps even act) so differently. When one considers the environmental conditions of Zeal, it was obviously a magical society. Because Zeal expected its royal family to be well-versed in magic, and Schala performed magic on a regular basis, her epigenome would have expressed exotic, magical traits (like blue hair, especially if magical ability was located on the same gene as blue hair color) and suppressed traits that might be considered non-magical. Also one should consider that she presumably lived a fairly comfortable life as a princess.
After being taken to the Darkness Beyond Time, she created a genetic clone of herself, Kid, and sent her into the world. While Kid is genetically the same, she would not possess Schala's epigenome (unless Schala impregnated herself with her own clone, then carried her for nine months and gave birth, and even then Kid would only inherit a few epigenetic traits, not the entire epigenome). And same as with the cloned cat mentioned above, Kid does not look much like Schala. Kid's epigemone developed under different conditions. Having not been raised in such a magically demanding environment, her epigenome would have no reason to express such strong magical traits at the exclusion of all non-magical traits (perhaps accounting for Kid's strength and agility, as well as her blonde hair and blue eyes).
At this point, magical ability appears to be genetic, and not epigenetic. If it is genetic (as I tend to believe) and therefore present in all modern humans to some degree, then even though Kid has the same magical abilities of Schala, her environmental conditions have caused her epigenome to suppress most of these powers (since she is not even the strongest magic user in CC). If magical ability is epigenetic (which seems unlikely, since magical ability is passed on to the next generation, at least in the case of the Zeal royal family), Kid wouldn't have Schala's powers at all, since her epigenome developed in complete independence from Schala's.
Another point worth discussing is Schala's change in appearance from CT to the end of CC. We know that Lavos can absorb and change DNA. Perhaps he did not change Schala's genome when he combined with her (a move that could potentially kill her), but rather edited her epigenome to make her more compatible to the combination process. The change in her hair from blue to blonde, and her eyes from green to blue, is completely possible with the changing of the epigenome (since both hair color and eye color are genetic traits).
Comprehensive Hair Dye
The people of Zeal did not simply dye their hair blue, or Janus would have lost his hair color as well after training with the Mystics. One may object that he dyed his hair even in 600 A.D., but even his Chrono Cross shell (Guile) has hair intended to be naturally blue and purple.
This theory contends that the hair of the people of Zeal appears blue when they are charged with magic power. It holds that when magical power is lost, the hair turns back to blonde. Why, then, did Magus's hair not turn blonde after he summoned Lavos and later challenged the beast in the Ocean Palace? Why didn't Schala's after the entire ordeal lapsed and she only had enough power left to transport the party out? What about Queen Zeal? One can argue that these instances were neglected because the developers did not want to make blonde sprites and palettes. Even at this stage, however, it is a stretch.
From: Theory (People)