Metroid Prime 1 is my favorite. It has a lot of atmosphere, great gameplay and beautiful graphics. And not only is my favorite Metroid game... is also my favorite game ever.
The worst is Metroid Prime Hunters... it doesn't feel anything like Metroid. Even Metroid Prime Pinball is a lot better than Hunters.
In order:
Metroid Prime
Super Metroid
Metroid Zero Mission
Metroid Fusion
Metroid Prime 3
Metroid Prime 2
Metroid II
Metroid
Metroid Pinball
Metroid Prime Hunters
Is definitely my favorite series.