Symphony of the Night without a doubt. It built on everything Metroid was and advanced so far beyond it.

Super Metroid, by far the standard setter.

Definitely SotN, but you can't go wrong with either.

Super Metroid. And Fusion is very close to SM level, especially for a GBA game.

Fusion was nowhere near as good. It held your hand through the whole thing and completely destroyed the open world exploration concept. Luckily Metroid Zero returned to form and was a fantastic 2d metroid.

Super Metroid. Symphony of the Night stood a chance, until I heard the voice acting.

 exactly. for gba, i did like metroid zero better than fusion

 fusion just didnt feel right. absolutely linear

SOTN, very easily.

I have yet to play SotN. I keep meaning to borrow it from a friend, but I always forget.

Metroid Fusion is kickass, but the gameplay isn't quite tight enough to push it beyond Super Metroid. I really liked the storytelling in this game, though. A lot of people were put off by the computer telling you where to go, but all it really did was give you a goal, you still had to figure out how to get there, and find all the secret passages and items along the way. Brilliant design IMO.

The problem with the 'fusion took away all the exploration argument'' is, imo, you only explore the game the first time.

Was Super Metroid worse on your 2nd/3rd/so on playthrough just because you knew the world? No.

Fusion doesn't hold your hand, it gives you a directive, and like entroper says, you figure out how to get there, and find hidden stuff on the way.

I'm not sure if I'd say it's *better* than Super Metroid, but it definitely holds its own.