From the very start, Metroid was built to encourage speedruns, even if that term didn't exist until a decade or so after it first came out.
When it was released in 1986, it was one of the first games to feature a completion time, with a special surprise for those who finished the game the fastest. It was basically an open challenge to gamers to try and finish the game as quickly as possible - the home equivalent of the high score craze that dominated arcades in the '70s and '80s.
Metroid was like The Legend of Zelda in that it gave players the freedom to explore their surroundings and backtrack, but required specific items to advance. Thus was born the concept of sequence breaking, which burst into the public gaming imagination with Metroid Prime, where the term was popularized. Soon everyone was trying to record the fastest possible times in Metroid Prime and its predecessors, with sites like Metroid 2002 serving as a guide for the techniques needed to finish the game without all of the required items.
Nintendo took notice. In 2004, they released Metroid Zero Mission, which is now available on the Wii U Virtual Console. A remake of the original Metroid, it brought with it a huge number of new features, including cutscenes, Zero Suit Samus, and ledge grabbing. It was an experience much more in keeping with Super Metroid, effectively capping off what had become a de facto trilogy and giving those fans who had gotten into the series with Super Metroid a chance to see where it had all begun (and even play the original Metroid, which was included as a bonus). This was a big deal in the pre-Virtual Console era, when the only way to play an old NES game was to dig up an old console, play a GBA port, or emulate it.
What really stood out, though, was the fact that Nintendo basically built sequence breaking into the game's design. Zero Mission is filled with shortcuts and secret routes, many of which will allow you to acquire items like the Screw Attack early. Freeze some wavers, and you can acquire the Varia Suit, or you can just ignore it entirely; take an alternate route to Ridley's lair, and you can skip Imago. You can even take a miss on the Long Beam, adding a bit of extra spice to what is otherwise a fairly easy game.
In effect, Nintendo embraced speedrunning with Metroid Zero Mission - a surprisingly forward-thinking outlook for an infamously conservative company. By its very nature, sequence breaking ran completely counter to the intentions of the original creator, stripping away the art of the design and revealing it as a mechanical construct. Rather than rejecting this approach as unnatural, though, R&D1's Yoshio Sakamoto found ways to weave a budding trend into his game's overall design.
If you think about it, sequence breaking is itself a natural evolution of Nintendo's original decision to include timed completion bonuses to Metroid. Making it a timed challenge encouraged players to find shortcuts, which encouraged them to develop techniques like infinite bomb jumping, then to exploit glitches like this one. By weaving sequence breaking into Metroid: Zero Mission, Nintendo not only acknowledged this trend, they made it part of their tradition of including secrets and shortcuts in their games - a history that extends back to the days of the original Super Mario Bros.
Naturally, dedicated speedrunners have since developed tricks to help them finish Metroid Zero Mission even more quickly. The best of them can finish it without collecting the Charge Beam, Long Beam, Wave Beam, Hi-Jump, Screw Attack, or even the Power Grip. Metroid 2002 has a long list of them.
In the years since, speedrunnings has evolved still further and become a fixture on Youtube and Twitch, putting Nintendo well ahead of the curve. Nevertheless, Super Metroid overshadows Metroid Zero Mission in the speedrunning community, a function of its enormous popularity. Still, it's an interesting footnote in the annals of gaming history - an instance in which Nintendo took note of a trend and decided to make it their own. It speaks to how comprehensive their remake of Zero Mission really was. It wasn't just a reskin of the original game, it was a top-to-bottom re-imagining.
With Metroid Zero Mission now available on the Wii U Virtual Console, now is a great time to appreciate this underrated gem. If you decide to pick it up, go ahead and see if you can skip the Long Beam. It's as good a way as any to celebrate what is probably Nintendo's best remake ever.