Super. No contest for me.

All of the Metroid Prime games are excellent, but I think the third one is the best. The level design was fantastic, I loved fighting the bounty hunters, and it had the best use of the Wii controller in any game I've played.

- It was too easy

- I prefer one big world as opposed to several smaller ones. Never the less, most worlds in MP3 were great. 

- Story wasn't as deep. The struggle between the Luminoth and the Ing was amazing if you took the time to read every single scan. The struggle between the conservatives and the modernists on the reptile planet in MP3 was also great though. 

Super Metroid was just too special for me, but I love every game in the series.
It's so sad the only thing I have to look forward to right now is a fan remake of Metroid II :(

            I am sure  that Retro is working on something Metroid-related.

No doubt:

1. Super MEtroid

2. Metroid Prime

3. Metroid Other M

The difficulty was a bit on the easy side but that didn't bother me too much. 

I loved the world in Metroid Prime 3, no complaints on that part.

It's a been awhile since I've played them but I don't remember the first two having particularly memorable storylines. At least no more so than the third one. 

Can't pass up Super Metroid, I can't remember how many times I got stuck and the amount of back-tracking exploring I spent in that game as a kid on the SNES.
Every new area I managed to get to, made me so bloody proud of my achievement. :P

I would not complain if there was a HD remake of it with completely remade assets.

Haven't really played the other Metroids unfortunately as my tastes in gaming shifted as I got older and thus by extension so did my primary gaming platform.

          You can always try the Prime  games on an emulator if you want.