A lot of it has to do with the fact that it's a slow paced FPS. That genre just works a lot better in a more fast paced setting, because slow paced FPS titles tend to feel very empty.
Some will explain this away using the highly pretentious label of 'first person adventure'
But that doesn't automatically make the formula any better than what it is.
Play Metroid Prime now, there's nothing really standout about it. At the time it had its pretty graphics, but today they are quite dated. Aside from tedious gameplay it is also very repetitive, scanning all sorts of things for dozens and dozens of generic messages, looking for that needle in the haystack. The flipping back and forth between scanning and shooting can make the game feel disjointed, and as clunky as the tank-like aiming controls.
Looking back on the game, it was very artistically pleasing in its time, but as a game it is just not very interesting. In my opinion, vastly overrated.
A new Metroid Prime from Retro? The team is gone, it would be an almost completely different team starting from scratch. As members of the original game left, even reviewers noted the marked decline of the second game, and then further decline on the third game. Next thing you know Retro is taking 3-5 years to make each of the two 2D Platformer games they've released over the last decade.