The two things that strike me as obvious when looking at Prime 4 are:
A) They should've copied Mass Effect, Halo, Rogue Squadron 3, or some other sci-fi for the exploration shit, instead of copying Breath of the Wild. Have Samus fly around in her ship or drive around in a space rover she "appropriates" from the Galactic Federation, and fill the places in between locations with enemies. Lots of them. Make it a war, if you have to.
In Mass Effect 1, sure, you have some sidequests where there's a great big plain full of nearly nothing to explore, but those are the sidequest missions; in the main missions, you have a gauntlet of enemies to trudge through on your space rover. Same thing with Halo and Rogue Squadron 3 in the ground vehicle sections: you have to drive or trudge through an area full of bad guys to shoot up. Populate the general area with life, and lots and lots of bad guys to shoot. Have it be the player's decision to either speed through them with a bike, fly over them with their ship, or blow through them with a tank. Or just hoof it on-foot, since we know from other games like Super Metroid and Other M that Samus has super-speed.
Maybe you can pull off a ME3/Battlefront-hybrid thing and have command posts be under Pirate or Federation control, and you will have an easier time in some of the dungeons (read: less enemies) if you clear out command posts controlled by the Space Pirates that are near the dungeons.
You can even put in a little bit of bounty hunting by having the Federation post bounties of top Space Pirate officers for Samus to capture or kill, and the rewards would be extra life energy/missile extensions. Or have certain artifacts the Federation wants to obtain, that are not central to the main story but would still net a nice reward if Samus gets them.
B) The story of Metroid Prime, the trilogy, was always about the titular "Metroid Prime", which you encounter on the first game in Tallon IV, and who then becomes Dark Samus, whom you fight in Prime 2 and 3. The story had a nice three-act structure that was neatly paced in the three games, and it ends with Dark Samus' death in Phaaze at the end of Prime 3. It began with the Metroid Prime, and it ended with the Metroid Prime's final demise.
Making a Metroid Prime 4 makes no fucking sense, not unless you're willing to revive Dark Samus and have her be a big threat all over again. Which, obviously, they did not do. The story has nothing to do with the titular Metroid Prime, which means that calling it "Metroid Prime 4" makes no goddamn sense. They could've named it something else, like Metroid: Hunter's Revenge (referring to Sylux as the hunter) or Metroid: Dunes of Discovery.
Also, Samus' motorcycle was named after Bayonetta's daughter in Bayonetta 3, another Nintendo-made game with Marvel-esque characteristics, what with the bad guy having Dr. Strange powers fighting a multiverse of Bayonettas. Nintendo is getting awfully self-referential with these names. It's like when James McCloud appeared in F-Zero, even though that is the name of Fox McCloud's father in Star Fox.