I've read several pages here dealing with the differences between Schala and Kid, and how could they be possible if Kid is simply a clone of Schala. Thanks to a newer branch of genetics, called epigenetics, we might be able to finally explain these differences, as well as Schala's change in appearance between the end of CT and the end of CC.
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, ect.
In fact, a calico cat named Rainbow was cloned. However, her clone looks nothing like her, despite being a precise genetic copy (
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1360161). Why? Epigenetics!
More about epigenetics here:
http://www.pbs.org/wgbh/nova/sciencenow/3411/02.htmlShifting 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).