Celestia and Luna care for some of their non-maniraptor subjects, whose identities are reflective of different evolutionary histories.
Many of the ancestral characteristics of reptiles are adaptations for life in warm, dry environments, from their aglandular, scaly skin to their tendency to excrete waste as pasty uric acid instead of liquid. Mammals, on the other hand, probably spent most of their history under the cover of darkness, hence the loss of good color vision and a greater reliance on olfaction in most mammals. (Derived primates like us had to re-evolve good color vision, and even then most of us have fewer color receptors than many reptiles.)
Today, long after the K-Pg extinction allowed mammals to become the largest animals in most ecosystems, these trends still hold, as the majority of extant reptiles are diurnal while the majority of extant mammals are nocturnal (or at least remain active at night). This is even reflected in the original cartoon, in which Celestia's pet is a bird (though a mythical one) and Luna's (if the official comics are anything to go by) is a mammal.