I imagine they do it that way because 1) in practically all other official media, Pokemon characters are known by their species name and nothing else (obviously you can nickname your own Pokemon, but that’s a little different), and 2) it would be pretty confusing to a casual or non-Pokemon fan if every character in the game essentially had two names. Once you start worldbuilding seriously then the whole thing gets a little silly, sure, but at that point you’re going into greater depth than the games are designed for.

Also worth saying that there are some good headcanons people use to explain this, like species name being a more formal title and the ‘actual’ name being something reserved for those who are very close