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 think they were asking for the franchise not the Metroidvania style of game.
That said, Hollow Knight has finally gotten its hooks into me and will not let go.