Not really. A Metroid reboot need be no darker than Prime was, which wasn't especially "dark" itself. For an open world game on the Wii U, XCX has damn good visuals, and it has plenty of serious moments. A modern Metroid "reboot" wouldn't need a grim-dark story with Samus brooding all the time and no light moments. This isn't the 90s. If anything needs to change, it's the game design. A new Metroid ought to be bigger, less linear, more open. Personally, I've always thought Metroid would work extremely well with an open world space-sim overworld. Flying around the galaxy and docking with randomly generated abandoned ships and space stations floating between planets that make up the core game's content. Maybe land on asteroids and explore abandoned mining facilities, attacking pirate moonbases for bounty, etc. In addition to the usual first person exploration and puzzle solving of the Prime games, of course. Ambitious, but totally doable by today's Nintendo.
XCX has comic relief, but then, it's also about the near extinction of humanity. The whole story is about as grim as you can get without making something that's just dull and depressing. While I haven't beaten it yet, I expect we win.
I wouldn't know about Prime being "sombre". The game barely has any story to speak of. It has plenty of logs from the pirates, but those tend to be written in a dull, scientific tone that add flavor and atmosphere to the world. But there's hardly enough there to really call the game conisderably more "sombre" than XCX. The dungeons are dark and you spend the entire game by yourself, but that's hardly "somber".
XCX was full of both intentionally and unintentionally cheesy moments that Prime simply doesn't have.
Prime's darkness comes from everything from its sound design to its scan logs, (which include gruesome clinical descriptions of how Space Pirate corpses were killed) to circumstances, (gunning down wounded and dying Pirates aboard the Orpheon) to its focus on solitary confinement. Nothing in the game ever breaks or lightens this mood.
"This isn't the 90s" actually sums up why it should be dark; audiences these days prefer games to be serious.
And while XCX looks about as good as is realistically feasible given the hardware its on and the gargantuan scale and seamless nature of its world, the latter necessitates some compromises, such as simplistic character models. A modern Metroid would need to be more visually polished.