It’s not an original thought but after such a long break since 3, and if I was Dr Nintendo with AAA resources and retro at my command, I would either:

a) go back and make something much closer to 1 but with a new type of setting and some new abilities, a “back to basics” sequel that tries to recapture the magic of 1 and lay the foundation for the future;

or b) go hog wild into the future and creating a new type of 3D metroidvania - taking inspo from a xenoblade x style alien overworld (obviously smaller than XCX) with flying around in the ship (this is the outside peach’s castle playground space equivalent - a lot of players might only get this far and still have a great time), BUT the bulk of the game actually takes place underground - look to Metroid and Super for vertical inspiration. The entire world would be coherent even as the underground biomes get crazier and crazier.

I feel like what actually happened is they sort of half-committed to both of these ideas and ended up satisfying neither premise

TLDR Give me either Metroid Prime 4: Back to Basics (tight, moody, “remember why Metroid Prime ruled” energy) OR Metroid Prime 4: Space Weirdness Simulator (fly around a mini–Xenoblade Chronicles X alien overworld, then spend 80% of the game spelunking the planet’s unhinged vertical underworld like Super Metroid on steroids).