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?
Fusion has always been my favorite. I “want” to not like how linear it is compared to the rest of the series, but when I get started playing it again that never seems to matter to me anymore. And because of that game structure, the game is very well broken up into chunks of 20-30 minutes of gameplay at a time which makes it excellent for playing on a portable console. I played it on a borrowed GBA-SP for the first time back in the day, a few more times after that emulated, and most recently I’ve been playing it again on my Steam Deck within the past week, I’m like 2/3 of the way back through it again, just took down Yakuza for the Space Jump last night before bed.
Fusion is also a huge story point for the series as a whole. It introduces the X and by doing so gives context to the existence of the metroids. And seeing that referenced again later in Dread was maybe one of the coolest moments I’ve experienced in the Metroid series.
Speaking of Dread, that one is a very close follow up though. I was super hype for Dread when it released and it is one of few games in recent memory that completely lived up to that hype. I was a big fan.