LogFAQs > #969892448

https://www.youtube.com/watch?v=ZQ8xa4drduQ
One of them was gonna be an XCOM-style tactics game by Retro Studios on Wii set at the very beginning, with Samus as a fresh bounty hunter fighting alongside the Galactic Federation and other bounty hunters against Space Pirates. Would've used models and sounds from Prime Trilogy, featuring locations from all across the franchise such as Zebes and Norion. The game would've canonized Justin Bailey as the name of the military commander.

The portable Metroid game by Next Level Games leaked by a former art designer was actually a multiplayer deathmatch game called Project Valkyrie. First phase was on DS and was similar to what you'd find from Prime 2 and Hunters, featuring boss creatures that acted more like obstacles. It was eventually canned due to hardware limitations until they were told to resurrect the project after Luigi's Mansion Dark Moon. Phase 2 was the same idea but were given a console-sized budget, so they were able to more realize their vision. Mid-match collectible upgrades were also added in order to give players advantages, with destructible parts of the environment you could utilize depending on the weapons. Since Kensuke Tanabe still wanted a Metroid game with a story featuring the Galactic Federation, he went on to become director of this project and it eventually transformed into something vastly different: Federation Force.

The last one is Metroid 64, but nothing ever really took off. R&D1 was too busy making Virtual Boy and Game Boy games until Metroid Fusion, and an as-of-now unknown third-party developer declined to make it after Nintendo offered. Miyamoto wanted it made but unfortunately he didn't have a say in the franchise.