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?
Super is so good. The sound design makes everything gel together into a smooth slurry.
But, like good.
Metroid Prime is a masterpiece. The artifact hunt is a bit padding-y, but you’ll be backtracking to get the power-ups anyway.