I always feel like this collection will never get a Switch release not because of the motion controls in Metroid Prime 3 but rather because Nintendo does not want to give people all three of these games for $60. This is a company selling Miitopia for $50 and Skyward Sword for $60. Sure Metroid Prime Trilogy was $50 on the Wii but Nintendo of today would want to charge full price or near full price for each title separately.
It's tied to the marketing cycle of Prime 4, which got an indefinite delay. That's all there is to it. They aren't gonna break up the collection. It's a game that already exists.