Right decision, because releasing a bad Metroid Prime game could have done some serious damage to the future of the series. It's already had some really rocky roads with Other M and Federation Force, and it's only the Metroid 2 remake that's managed to get it back on track.
The fact Nintendo doesn't know what to do with Metroid on home console is quite worrying, as well, so it's only natural they turned to Retro, who has done it all before. The Retro team today might be different to the original one that worked on MP1, but it should at least be far better than anything Nintendo was about to churn out.
Nintendo itself just needs to concentrate on 2D Metroid. A HD 2D remake of Super Metroid with hi-res sprites, a "Metroid V" set post-Fusion. At the least, get all the past games playable on Switch in some form - a collection or individually released. There are plenty of things for them to do instead of fucking 3D Metroid up, so it's defo a good job Retro has jumped in.
It's really unfortunate, and I don't expect the game now for at least three years, but gives them enough time to ensure the Prime trilogy gets sorted. I hope they can work something out for Prime 3 on Switch, tho I don't know how they will get around the motion stuff and if it will convert to normal controls.