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?
FWIW, that room is completely optional, only reward is a Power Bomb Tank. If you fall down there you do gotta get out, but if you can at least make your way up to the first platform you can bomb it to reveal a tunnel that lets you bail.