Just because it'll be the end of Samus' saga, that doesn't mean it has to be the end of Metroid. As crazy as it may sound, they could always make a new Metroid game with a new protagonist with their own story/saga. Not every Fire Emblem game has Marth as the main character. Just like Shulk is not the main character of every Xenoblade game. They could always go that route and expand the Metroid universe beyond Samus Aran, which could open up a plethora of possibilities for story-telling and world-building.
But Samus is the protagonist of all metroid games unlike those other series, the only one where she is not is the unholy piece of trash known as Federation Force, Nintendo hasn't been giving Metroid AND Samus the respect they deserve despite having some of the most lauded games of all time with Super Metroid and Metroid Prime, while they could center on other characters like the ones from the Metroid Prime Hunters game or the bounty hunters from Prime 3, Samus always had a perfect way to showcase in universe, moreso in some games than others, both the human perspective of things while also being very natural to the "alienish" things, she travels to places the humans of the Federation will never have a chance to survive, and that was originally the concept behind her primarily being contracted to deal with shit impossible to them like the space pirates, so i think we could have more Metroid games with Samus since Nintendo seems to like to put her on hold for very long periods of time and forget the anniversaries of her game. And while we are at it, Nintendo could make something with F-Zero, Kid Icarus, and stop resetting the heck out of Star Fox, at least they showed another Wario Ware game.