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.
I know a lot of people, myself included, got frustrated with the EMMI sections. Unless we all missed something about how they work, that the game could stand to explain better, you could end up walking into the room with bad RNG and the thing could be right on top of you. If you're speedrunning the game, presumably you have a trick to avoid that scenario, but it was quite common and brought down my opinion on the game, for sure.