Deer Force Knew
Examples of things in the game that are evidence they were thinking ahead to the modern state of speedrunning the game. Whether it's evidence that a "glitch" was actually an intended feature, or small elements of the design that enable a smooth flow of full-speed movement.
Some of this "evidence" is obviously just coincidence, while some of this is very probable as intentional design.
Speedrunning
When asked in this thread about how he felt about sequence breaks like climbing Bubble Mountain to get Speed Booster and Wave Beam, programmer Yasuhiko Fujii gave this answer (as poorly translated by Google):
As for the shortcut, as a real thrill of metroid, Introducing the time system, those who are time trial, beneficial Like I am against you.
As a result it's obvious that competitive speedrunning of some sort was intended, along with some sequence breaks.
RBO
The very existence of RBO as a No Major Glitches category is often debated as to whether it's intentional design. In most other games, Reverse Boss Order requires game-breaking glitches to Wrong Warp to the end of the game. These include Donkey Kong Country, Zelda 2, A Link to the Past, and many others.
To reach Ridley, the only question is whether Lava Dive was intended, and it seems plausible given the difference in physics between lava and water; a similar set of walljumps through water would not be possible, so the geometry of that room may have been chosen to allow for a tough set of walljumps to be possible.
The Draygon escape is a tougher question: early runs of the category would have Draygon carry them to the top-right platform before killing her, and then X-Ray Climb through Precious Room. X-Ray Climbing does allow for out-of-bounds travel, but on the other hand it's quite analogous to the "Door Jump" from the original Metroid, so an argument can be made that it was an intentional homage.
Mockballs
The exit of the Power Bombs area in Green Brinstar Main Shaft allows for landing on the top ledge if you mockball through the tunnel.
