My favourite Metroid game has got to be Zero Mission on the GBA.
A weird choice maybe but it was my first metroid when I played the GBA, I thought the music and atmosphere was kick ass and enjoyed the simple enough controls.
For a 3D Metroid it would be the trilogy on Wii at the time.
What about you?
For me, it’d be Prime. The game just oozes atmosphere from start to finish, and has one of my favorite game soundtracks of all time. I still sometimes listen to the Phendrana Drifts tracks because they’re just so damn chill.