Fusion. The atmosphere is the best a mainline Metroid has ever accomplished. Everything is designed to make us feel in constant danger and even scared: from the presence of the X parasite to the SA-X always trying to hunt you down, the plethora of dangerous and unexpected situations (elevators that lose power half way; boilers about to make the whole station explode in a couple of minutes; the shadow of a mysterious giant monster flying on the background; a sudden power loss that makes doors and saving stations not working... The game is constantly trying to make sure that you don't feel in control of the situation at all. It wants you to feel nervous, scared and in tension. And Metroid Fusion does this flawlessly.
People don't like it as much as Super or Zero Mission because it's far more linear than any other Metroid. And while I see their point, I don't think the linearity of Fusion is a bad thing per se. I think this structure is perfectly justified and it never makes the game be "less" than other entries. Just different. And there's A LOT of stuff to collect anyway. Plenty of backtracking when getting new power ups in order to get missile expansions, energy tanks and other secrets... and many of those are very well hidden or require an interesting test of ability. So while the main story is linear, the game itself is packed with content and secrets.
Fusion also has the best story in a mainline Metroid. In the grand scheme of gaming, Fusion is nothing out of this world. But as a Metroid game... it really blows away the others. You get to know some of Samus thoughts and feelings just enough to not feel intrusive while helping to connect more with her. Also the whole Adam/Federation/Metroids/X Parasite situation is very well handled and is followed with a lot of interest. And the game has a great ending. Very emotional.