I can't beleive I never thought of this thread. Ok my favorite is  metroid for the nes the first metroid game. I liked it because It was the first game that I played that was not too linear , and if that game wasn't made I wouldn't have my favorite video game series. So what is the best metroid game. If this thread was done already there could be new people to answer so please don't post "this has been done already".

 The fpa's still pertain to the story and are part of the series. The prime miniseries is part of the larger metroid series and still count. 

Fusion, because Samus actually had a personality and character development. The gameplay was good, too.

 Fusion was good , you also see character development in corruption a little. How she feels sympathy for the other hunters. 

Prime 1 and Fusion are the best I have played yet, but I have not played Metroid 2, Super or Prime 3

i thought Corruption was the best IMO - loved the gameplay

Actually, that was more of showing her character. She didn't actually grow in terms of character because she didn't have a noticeable personality in the first place due to the fact that she never spoke a single line in the game. If anything, Prime 3 should have developed the other hunters, which Retro failed to do. 

I say Super Metroid is the best. It was the first Metroid game in which Ridley had his "Traditional" moves and appearance, the same goes for Kraid. Also the fact that it had so many power ups made it awesome and when your health reached zero you actually saw Samus out of her suit!!! :D