I hope for Metroid 5 they go a different, yet interesting way of losing her powers. I was thinking maybe space pirate find a way to take her suit and you have to find the pieces and reassemble it, starting from zero suit. Could even add other experimental chozo artifacts and have them all placed in branching paths from a central point, to make it feel like theres more freedom and exploration.
Or idk more suit permissions.
The best way is to make them new versions of the powers. Prime 2 could have done this given how many new powers it had, Samus never 'lost' the dark or light suits or beams, they were brand new. So you start in the new planet/environment with the Varia suit, but it's not very useful there, you need to get the plasma suit and crush missiles or whatever.
Or just don't deal with it at all. It's a video game, and a series that IMO isn't afraid to be a game. Don't hand wave it, just skip it, start with no powers and leave it at that. It's silly but so is Bond changing actor, you get over it after 5 minutes.
Prime 1/2 had the introductions where you can certain powers to do a tutorial then lost them so needed an explanation, but every other game it was unnecessary.
Well they have to deal with it. Samus isn't going to be getting work after she became a terrorist in Fusion. She needs to clear her name and expose the conspiracy first.
Metroid also has a history of covering large story beats in an intro/manual.
The intro to Metroid 5 could be 'As shown in Bottle Ship/SR388 ship, a group in the federation was evil
[recap screen of OM/Fusion scenes]
I delivered the information to HQ and those responsible were taken into custody
[shot of scientists being arrested]
I received a new ship as thanks, and was off to search for new bounty and Space Pirate holdouts.
[shot of new ship]
When I received an alarm... An explosion at a federation base on a nearby planet!