Let me start by saying I disagree with the calculations in the OP. There's no way Breath of the Wild's budget was $60M, let alone up to $96M. I'd say it was $40M max, but possibly even closer to $20M. So I expect Metroid's budget to be less than $20M.

....But you asked what I would I. I would definitely spend more. I'd say around $30M. I've always thought that Nintendo should spend more on their games, but as mentioned, they are indeed very cost efficient, so that's why my recommendation is still a modest one.

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