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.
Runners will often say "Deer Force Knew", either jokingly when referring to a mechanic that's obviously not intended, or when truthfully remarking about a cool mechanic that they're showing appreciation for.
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 shortcuts, the real pleasure of Metroid is that I would like it to be useful for those who have introduced the time system and time trials.
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: to even get to Botwoon without Gravity Suit, you need to either do the Ice Clip through Botwoon Hallway, or use a stored shinespark (either Blue Suit or Spike Suit). Additionally, there's the matter of escaping Draygon's chamber. Early runs of the category would have Draygon carry them to the top-right platform before killing her, and then X-Ray Climb through The 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 could be 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.
Crossover Randomizer
The combined Super Metroid and A Link to the Past randomizer was made significantly easier to put together as a result of the ROMs having absolutely no overlap. Could Deer Force have predicted the existence of the combined randomizer?
One theory is that Nintendo may have made a small number of carts with both games in order to show the games at trade shows. So far there's no evidence for this, but it definitely seems plausible.
Visual Cues
A number of advanced techniques have visual cues in either the foreground or background in order to help the runners with timing their inputs. Examples include the foreground stalactites used for firing at the door for the speedball in Terminator, or the debris on the ground used for short charges and X-Factors in Draygon's Room.
