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?
If we’re allowing Trilogy as one game then I’m going to step out a bit and go with AM2R. It’s extremely good and not “for a fan remake”, just straight up good.
If we’re talking single games made/published by Nintendo I’d go with Dread for 2D. I played through that 3-4 times back to back when it came out which was a totally new behavior for me. For 3D it’s Prime 1, still the best 3D example of the genre.