>>52718406Except latias, and many other pokemon have displayed intelligence and cognition far greater than regular animals, latias is even shown at one point being capable of understanding the meaning of full on human sentences when she nods to a question by the old man.
She seeks out emotional solace/comfort with someone she trusts when her brother gets kidnapped, and is capable of grieving, all these things and others display a level of intelligence far greater than that of regular pets.
Literally the only reason why this would be zoophilia is because of the prospect of a human having sexual intercourse with a non-human, and even then it would be xenophilia rather than zoophilia due to the blatantly human level intellect and cognition displayed by Latias throughout the film.
And this problem can actually be avoided somewhat easily whilst also adressing a lore issue in regards to why people in the pokemon universe have no idea where pokemon eggs come from, despite them paying a close eye on them at the daycares, and its because pokemon eggs arent created by a male and female pokemon merging their genitalia in order for the male to ejaculate his gametes into the female reproductive areas and subsequently merging the the females gamete, but rather it is created by affection out of effectively thin air or aura, basically when 2 pokemon of compatible inverse auras 1 male and 1 female, experience deep affection for one another, their strong aura fields that they are projecting as a result of them experiencing said affection results in the eventual manifestation of a pokemon egg with the characteristics of both its parents, aswell as some of its own from gained from the environmental aura.
TL;DR When daddy Pokemon and mommy Pokemon love each other very much, an egg is created out of effectively thin air
