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Blah, I hate the Wii version. Its the game that truly coined the whole Wii "waggle" un-phenomenon. I'd only recommend it if you have (or want) Parkinson's. My wrists hurt so much, I'd switch the wiimote/chuk to the other hand for awhile. Let's not forget that the motion controls are also pretty unreliable, so trying to do any specific move can feel like a crapshoot at times.
But what really irked me was that there is only 1 button available for using sub items. You can "equip" 3-4, but only have 1 available at any time... you have to switch between the 3-4 with the d pad, then hit B or whatever to use it (been awhile, I forget exactly). Sounds like nothing, but I found it to be absolutely rage-inducing. Like why couldn't the dpad just use the item right then and there? Pointless. Its like adding a second menu to switching items. Cube may only have 2 open slots to mess with... but thats 100% better than 1, and as petty as that sounds, it certainly makes a huge difference in the long run.
The only pro I will give the Wii version is in its aiming controls, which are near perfect... but ultimately not a big deal considering its not needed too often. Some may say widescreen support too... but it stretches the resolution to achieve that, thus making it technically uglier (though aesthetically more pleasing I guess). I call that a wash.
Gamecube may not revolutionize anything, but its all tried and true. Wii takes one step forward and 10 steps back.