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?
I’ve seen some mentions of AM2R, which I love, but also wanna shout out the romhack Super Metroid Redesign.
Its hard for me to pick an absolute favorite, but Fusion probably gets it today from me.