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Hilda is the correct protagonist for thematic reasons.
Yin and Yang represent many dualities, but one of them is the duality of genders.
Yin, the black one, is female, and Yang, the white one, is male. But Zekrom appears more masculine and Reshiram appears more feminine.
Notice how Hilda is a tomboy (masculine female) and N is a twink (feminine male)? Reshiram and Zekrom represent them.
And in addition to this, Hilda's name is White in the manga, and was called Whitlea and Shiro in pre-release material. Uncoincidentally, White version is the version where you catch Zekrom.
And N stands for Nigger, which is an American word for "black". And Black version is the version where you catch Reshiram.
Hilda being the protagonist is not only ideal, but it's also the truth.
