If by "dark" you mean "parts of the game are pretty darn dark" than I agree. Otherwise, the game doesn't really fit any of those criteria.
I'll admit the opening of the game, on the half-destroyed pirate vessel, is a little grim. But pretty much all of the violence and unfortunate happenings occur against these ugly looking enemy creatures. I wouldn't call that grim.
The game also isn't especially ambitious in scope or technology. Where the game excels, is how it translates the 2D Metroid formula into 3D. The game has AMAZING design, but as far as the scope or technology goes Metroid Prime was fairly modest in 2002. Ambition isn't what made the game great.
I also don't see how making a darker "Paper Mario" would solve people's problems with Sticker Star's game design. TP's style is pretty widely considered to be kind of ugly by today's standards, especially in comparison to the more cartoony look of its predecessor. Making a sequel to Super Mario Galaxy doesn't require "guts" when the template has already been utilized and proven twice on ancient hardware. Nintendo probably hasn't made another Metroid because Other-M has been reviled by a lot of people, and Retro's been busy with Donkey Kong Country Returns (the first of which sold way more than any Metroid title).
It proves that Nintendo is still completely capable (and certainly has the "guts") to fund and making grim, beautiful, ambitious games. Nintendo's never really made many of these types of games. Even Metroid Prime, I wouldn't really call "grim" or "ambitious". Where it excels is level design and atmosphere.
A Metroid reboot for today's market would have to be significantly darker and more visually polished than XCX. It would need high end graphics, (or at least, as high end as the platform allows for) and a more serious tone.
Prime is considerably more sombre than XCX; there is no comic relief, no bubbly characters, no cheesy moments.
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".