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If BOTW needed 2 million to be profitable, they could invest the same amount in Metroid; a top notch HD Metroid with excellent production values could easily sell over 4 million and become the new highest selling game in the series, factoring in that Nintendo's franchises tend to sell better on Switch than ever before.
Plus, as Pemalite pointed out, its not just the profits from sales of the game, but also that such a game would expand Switch's appeal and sell systems to people who would then go on to buy other games for their new Switch. There's tons of players out there who wouldn't buy a system for Zelda or Mario, but would buy one for an epic mature sci-fi adventure, and once they have the system they might then decide they may as well pick up BOTW and Odyssey.
Reaching new customers is critical to maintaining a healthy and growing userbase, and Metroid Prime 4 done right could win over gamers who currently have no reason to buy a Switch.
