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?
It’s really hard for me to name a single favorite Metroid; I love most of them. In terms of non-linear open exploration, Super Metroid is probably my favorite, followed by AM2R. But I also really enjoyed the boss fights in Metroid Dread; they were really challenging…for me at least.