This is a game that it's hard for me to be objective about because of formative it was for my love of games as a medium. Luckily, it's basically impossible to overrate this game so imma just roll with it.
The level of fanaticism that must have gone into this game is genuinely staggering. Details like seeing Samus's reflection in the visor or having certain enemies create visual noise if you get too close is on such a level that I can only respond with genuine awe.
Running around the areas with the amazing soundtrack and the beautiful surroundings is truly a magnificient experience that very few other games have ever managed to capture. The joy of exploration that comes from this, along with lorebuilding that comes with scanning your surroundings leads to such an incredibly immersive experience.
On top of this, the gameplay is both unique and extremely compelling. I remember hearing complaints about it at the time but what can I say, I never had issues. The lack of fluidity in movements that stems from not having a classic dual-stick FPS layout helps to both emphasise Samus's position as someone who is ultimately stuck piloting a kind of mech suit but also places even more emphasis on the surroundings and creatures that you encounter. You are truly encouraged to take in every blade of grass when adjusting your aim takes 5 full seconds. Cop out? I don't think so, when the game ultimately isn't made to require quick jerky movement then I don't have any issues with having a control scheme that emphasises what it is that I already love about the game.
Then yeah, the combat and platforming. I love it! I think it's kind of amazing how fluid it feels to move around from one platform to another. The combat is all balanced around the movements that you have access to and it makes excellent use of it in every fight.
Many, many beloved games have caveats like "yeah, but this section sucks" or "the fact that you have to do this in this way is a bit annoying". Metroid Prime is pretty much completely devoid of moments like this with the possible exception of hunting down every artifact. I personally never had an isssue with it but I can at least see the complaint.
So yeah, I'm done gushing. I love this game, it's one of my all-time favourites and I can't in earnest find a single bad thing to say about it.