There is an unused scan image of what looks like a Shinesparking Samus. In an interview with Retro Studios, it was revealed that they were considering implementing the Speed Booster and Shinespark, but due to the difficulties implementing it, it was scrapped.

Kraid was intended to return as a boss, but was scrapped due to time constraints. Kraid's character model was completely finished, but the there wasn't enough time left to create a fully polished boss fight.

"It was decided that Kraid was not imperative enough to the Metroid Prime project to run the risk of pushing up the release date in order to fit him in." -Gene Kohler

During development, a flying insect-like enemy was removed from the game. It is speculated that it may have been an early design for the aerial pirates or possibly intended to serve as a boss at some point in the game.

During development, a four-armed gorilla enemy, possibly intended as a boss of the ice area, was removed from the game. Nintendo felt that some of the early models looked too much like monsters designed for an RPG and decided they did not fit in the Metroid world.

The development of Metroid Prime started with an original game Retro Studios was creating for the Nintendo GameCube titled "MetaForce". The game was initially a third-person action-adventure game starring three genetically modified women with different playstyles that made up the titular MetaForce. They consisted of a cyborg named Brynn, a psychic ninja named Miko, and a rifle-wielding assassin. The game took place in a near future world where gene editing had become inexpensive and common. It would have had three 10-hour chapters, each with its own antagonist that acted as an arch-nemesis of the one of the girls. Chapter 1's villain was a Luddite cult leader terrorist who used gene editing to create an army of four-armed mutant foot soldiers. Chapter 2's villain was a Nazi eugenicist who wanted to steal the MetaForce girls' DNA to engineer "a master race of hotties". Chapter 3's villain was a mind-controlling South African who was the mastermind behind all of the preceding events, which were intended to be a distraction from his true plans.

Retro Studios received conflicting feedback from Nintendo of America and co-producer Shigeru Miyamoto. NoA asked them to switch to a first-person perspective, cut any two of the girls, and improve the remaining girl's controls, leaving Brynn as the sole protagonist. Miyamoto then told them that he felt Brynn was too generic of a protagonist and was uncertain about the game being a first-person shooter. From here, the team would switch back to third-person and completely rewrite the game. It now took place in the 1970's and starred an alien protagonist that the United States government had discovered in a crashed UFO. A government team called "MetaForce" then raised it as their own to combat another evil alien race planning to invade and enslave humanity. One day out of nowhere, Miyamoto commented that the game's new alien designs would make for great Space Pirates, and asked the developers if they would prefer to make a Metroid game instead. They agreed, and MetaForce was cancelled in favor of what would become Metroid Prime.

According to one of the game's tech leads Jack Mathews, shortly after Metroid Prime shipped, Nintendo told Retro Studios that a "bad batch" of GameCube CPUs shipped, and apparently this game was the only game that misbehaved on them. Upon seeing videos of the issue, it became clear to them what was going on:


In retrospect, he wondered if it was possible to instead rig up the GameCube so it stayed in the freezer and let the wires run out to connect to the TV to save time running back and forth.

On the more technical side, Mathews explained:


When a player called Nintendo of America's support hotline about this animation problem, they would send them a new copy of the game disc with this updated code.

When this story was posted to Twitter in 2022, one user posted an older video of a graphics glitch positing that the issue is "caused by the ANCS file using the wrong CSKR for the suit model", and that it might be possible to simulate the issue outside of the hardware and software conditions it originally happened in. Mathews replied:


Mathews also talked about how it would have been a bigger hassle to rewrite the skinning pipeline to use the locked cache, because it would have been a rewrite by taking the risk of adding new code and may have net slowed things down. Adding the NOPs wouldn't break anything and just moved the stalls from the memory controller to the PPC chip.