Being a big fan of the older Metroid games (Super Metroid is my fave game of all-time), I bought a Gamecube years ago to play this game. However, at the time, it was too different to really get into. I played for a couple of hours but then didn't pick it up again. 
 
However, I'd like to give it another shot and since it's been so long since I played it last, I'd have to start at the beginning anyway. 
 
My question is is it better to play this on the Gamecube or would I be well advised to pick it up for the Wii and play it there? 
 
Thanks!

Gamecube the c stick makes switching between weapons so easy that you can do it mid battle witch makes the shooting more fun instead of worrying about stabilizing your hand and finding the perfect spot for the wii remote

The Wii version is the better version.
MP on the Gamecube was my favourite game period, and it's made even better on the Wii.

I've preferred playing it on the Gamecube but that might just be because that was where I first played Metroid Prime. I suppose it comes down to whether you feel more comfortable with the Gamecube or the Wii controller/s.

Play it on the 'Cube.  Yes, the controller design sucks and your wrists will hurt after a while but it's a much better experience on the gamecube.

I'd argue Wii but then I played 3 first then went backwards so.... All depends how used to the Wii remote you are. Its pretty intuitive in both instances but if you're up on your aiming and moving with the Wii controls then go for that. In either case the Prime trilogy on the Wii is pure gold.

I prefer the wii. 
 
You also get three games.  C'mon.

I prefer the Wii versions, mainly because they have 16:9 support. Aiming is much better in the Wii versions. And you can aim and walk! :O

You can unlock the Fusion Suit in either version, but the use of the Gamecube GBA Link cable is what seals the deal for me.

I am playing through them on the Wii right now, having never played them on the Gamecube. 
My experience? The controls are fantastic. There is no real motion-control jank that might be expected from lesser games. Changing weapons is real quick, though I guess it's almost instantaneous with a gamepad. 
But whatever, you arn't gonna notice that! 
 
Also, 3 games for the price of 1! 
Also, widescreen, whereas the Gamecube ones will stretch weirdly on widescreen TVs. 
Also, the Wii version incorporates an achievement-esque system that was apparently in Metroid Prime: Corruption (I had no idea, I'm only up to Echoes), so when you do things like defeat bosses, 100% explore areas and such, you'll get a little achievement, which you can then use to buy things like artwork, soundtracks and other stuff like that from the main menu.  You wont get those for Prime 1 and 2 if you play them on the GC. 
 
Edit: Oh no, perma-bold strikes again. Don't worry, I'm not actually shouting this information at you. OR AM I
 
Go for the Wii version!
 
@SethPhotopoulos said:

" I prefer the wii.  You also get three games.  C'mon. "

 Bump to knock this down the list due to a bug in the forum.