Prime is not trying to be an FPS and it benefits more from being a more slow, methodical game rather than a fast paced one. Focus on speed and action is one of the reasons why the level design in 2D metroids deteriorated after super (and why prime 3's wasn't as good as 1/2s)
It really doesn't, the 2d Metroid games were always pretty dang fast, the entries of declining quality didn't really change anything there. What they changed was the heart of the series, the world and progression design.
The team could still do it in fusion. There was a secret room you could only get to with very skillfull sequence breaking. But it literally only existed to slap you in the face and tell you to piss off and follow the path, and only the path. They knew what they were doing in zero mission when they had very precise alternate sequences and practically no actual sequence breaking (even if you did, your power up wouldn't activate).
And prime was not immune either. There was a huge disconnect between NA and the PAL prime base, because they both played different versions of the game. PAL users could not explore or sequence break at all compared to the original NA release, nearly every neat thing that was found that allowed a player to express their agency and leave the beaten path, was surgically removed (upon original release, players choice and subsequent releases gave everybody the nerfed version, as did trilogy).
Speed and action in games like corruption, fusion zero mission and other m wasn't a cause. It was at most a byproduct. It wasn't just Metroid that was facing this deteriorating either, every Nintendo game with remotely similar attributes was circling the drain in the same way, including Zelda.
Aunoma finally let the cat out of the bag on this one in an interview after the success of breath of the wild.
It wasn't an accident. It was very much on purpose. He gave many interviews where he talked about 'breaking tradition's. In several of them he spoke about the company culture that had arisen, and become tradition, where the designer was supposed to control the game experience, control what the player does, and where they go, and when. And any time a player did something that was NOT what, where, or when they wanted the player to do it, they considered it a mistake, a glitch, that had to be removed...
They literally, actively, hated explorers, sequence breakers and stunt players.
And they did so voraciously, with increasing efficiency, from the N64 to the Wii u, all the way up to breath of the wild.
Today's Nintendo does not appear to be obsessed with the tradition of overbearing control that caused the deterioration of Metroid.