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Well, it was talking about the player, who can be either gender. I'd usually say "they" but that's not entirely correct for reasons I can't remember.

At least that's how I interpreted it; I wouldn't add he or she to just the pokemon, but in that case it would have to be consistent across the entire analysis, meaning no "it", right?

they refers to more than one person while player refers to one person - you can only use he or she when regarding the player. "it" is kinda awkward when used to refer to humans so it's unused, but "it" when referring to a pokemon is fine (neutral-gendered).

basically when you're referring to the player, pick a gender, but when referring to a pokemon, it's personal preference (though unless a pokemon is only available in one gender, "it" can make the most sense)