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Mr Khan said:

But it neither overwrote nor contradicts the Prime games (at least not directly. There's the implication that the Space Pirates were extinct after Zebes fell, but given that their homeworld was occupied in Prime 3, it falls in line neatly). There's a difference between not incorporating any of Prime's story and pretending they never happened, which largely falls in with the question of how could the game have incorporated Prime, story-wise?

(and he certainly acknowledges them to a point. Kinetic Orb Cannon, free Morph Ball jump as a standard feature, and multi-seeker-missiles)

I think the Prime games were as relevant as the first Metroid was, and that got mentioned.

I don't think that gameplay elements count as canonical... canonization