‘Third party code’ was to blame
Speaking to Kiwi Talkz YouTube channel, Prime developer David Kirsch [Zoid] explains that originally he and the team wanted to bring Super Metroid in because so many people were so passionate about it:
“I kind of missed the whole Metroid train. Once the re-org happened…that was complicated and messy, I got assigned to Metroid. And holy crap I missed [Super Metroid], this game was incredible. I played through it twice in three days…now I understand why people want this game.”
He goes on to explain how that led to an attempt to put it into Prime:
“I ported a SNES emulator to the GameCube and had it running, just for fun, and thought can we make this a thing? And we were like I don’t know we can ask. And Nintendo was like ‘hey that’s third party code’ and a bunch of other stuff, so they kiboshed that. But the gear started turning and they did have the NES emulation they had built for the GameCube, and that turned into bringing the original Metroid into the game with the game link…with Fusion.”
It wasn’t all for nothing, though. The Metroid Prime Super Metroid initiative was scrapped, but the team decided to compromise, and added the first NES game into the mix. As a reminder you can unlock the original through a semi-convoluted process that involves Metroid Fusion and a Game Boy Advance to GameCube link cable. Oh, and you need to beat Metroid Fusion.
The interview broaches a ton of subjects over the course of roughly an hour, so if you’re a Prime fan, it’s worth checking out.