Differences aren't always something that can't be vaulted over. It has a lot to do the circumstances that created the differences and how much someone is willing to bend. With animals it's all instinct as far as I know. But pokemon are smarter than normal critters and bond with their trainer. For a trainer, pretty possible they'll set it aside. Just need to work with them and treat them as equals.

One isn't better than the other and so on.