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MDMAlliance said:

Nowhere did Nintendo said "only."  If you read (and listen) closely, it is almost guaranteed to mean that people who have both versions wont have to pay for Mewtwo.  

Having finished the video, it's true that it's not as clear cut as stated in the OP. That said, it's incredibly ambiguous: if they intended to sell it as DLC to everyone, they certainly didn't doa  good job of communicating.