In a conversation with Kiwi Talkz, Developer Metroid Prime David Kirsch – AKA Zoid – has confirmed that this rumor is indeed true. Kirsch revealed that he only really played Super Metroid after being assigned to Metroid Prime, but loved it so much that he finished it twice in 3 days.
Because he was a fan of the game, he tried to load it into Metroid Prime, according to rumors. He also confirmed that it was indeed the unofficial nature of the emulator he was using that prompted Nintendo to ask for it to be removed – but Kirsch says his efforts eventually led to the original. Metroid replaced instead.
During the same conversation, Kirsch – who was referred to as ‘Zoid-O-San’ by Shigeru Miyamoto – revealed some more information regarding the development of Metroid Prime. For example, when Miyamoto saw the first prototype of Metroid Prime, he immediately noticed that something was wrong with the camera, which was placed lower than her actual height (he had a keen eye for detailed, clear).
Now-retired Kirsch admits that he worked 100 hours per week on the production of Metroid Prime and that he will be partnering with Retro Studios in part to develop Metroid Prime 3 because he was exhausted. During his 32-year career, he worked World Of Warcraft, Dota 2, Portal, and Quake.
https://www.nintendolife.com/news/2022/01/metroid-prime-dev-confirms-that-nintendo-blocked-the-addition-of-super-metroid-to-the-game Metroid Prime Dev confirms that Nintendo has blocked the addition of Super Metroid to the game