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They almost never use non-neutral pronouns for Pokemon. This is understandable in the first gen when nobody had a gender, and unintrusive enough in the main games afterward because none of them are recurring speaking roles.
But it really fucks with the writing in Mystery Dungeon. You have these long strings of monologue where you or your partner angst about each other, and using their full name each time. It really takes away from an otherwise very powerful ending because it breaks natural speaking cadence and sounds really wooden.