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Aiddon said:

Samus was nothing more than a Mary Sue, a player proxy that we projected onto. It's the same thing with Gordon Freeman, Master Chief, Marcus Fenix, Commander Shepard, and just about every protagonist in Western RPGs.

That is not what Mary Sue means. Mary Sues are an authorial self-insert into an established canon where they don't make sense. Silent protagonists are not Mary Sues, that assertion is ridiculous. Doubly ridiculous in that most of the characters you named aren't silent protagonists, have clearly defined personalities (Shepard, Fenix, Chief), and are clearly not authorial self-inserts.

Adam Malkovich is actually much closer to being a Mary Sue; a super important figure that Samus couldn't help thinking of as her father (to the degree that her being raised by the Chozo is rarely or never mentioned in this story), a person around whom the events of the game center in a way that's not characteristic of the series up to this point, a person who engenders out-of-character behavior in the protagonist, and who is the actual embodiment of how Sakamoto sees himself as Samus's father. Adam Malkovich is a textbook case of a Mary Sue; Samus, prior to this game, didn't fit the definition at all.