As the new episode progressed today, it was revealed that, in fact, wings and horns are genetic traits. If this be the case, then it is also implied that Earth Pony genes are dominant, and the others are recessive. So, therefore, pegasus can have earth pony children, unicorns can have pegasus, and earth ponies can have unicorns. So, my theory goes as such. The royal sisters were, in fact, born by a very rare genetic anomaly in which the genome is mutated to show traits of all three "races." This would also explain their difference in appearance to the other ponies, as their DNA is altered. The capacity for this trait to occur would only be present in the sisters' bloodline, so as to explain the lack of others like them.