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?
Dread. The movement feels incredible and I feel like its map naturally leads players to the next relevant area the best without as much backtracking and getting lost. Brilliant game.
The EMI segments with unfair BS kinda take it down for me a slight notch