If you want my honest opinion...
Pikmin 1I heavily recommend going Gamecube for this one. The control scheme, while it works, requires more patience than the gamecube controls, and since you're on a 30 day time limit(Which, in the Wii version, you can turn back the clock), you'll always have the feeling of being rushed, and with the motion-sensitive controls, it really doesn't do you any favors. I just find the Wii version of Pikmin 1 nearly unplayable for those reasons, which is unfortunate as I find the "turn back the clock" feature to be brilliant. Alas.
Pikmin: Gamecube EditionPikmin: New Play ControlPikmin 2This one, you could definitely go either way, and I actually own both versions. As mentioned before, the Wii control scheme is great for Pikmin, and unlike the original, Pikmin 2 doesn't force a time limit, so you can take your time to learn the controls and enjoy the scenery and such. While you can't turn back the clock like in Pikmin 1 Wii, the fact that you can reset the game in caves without having to get up and press the button yourself is a total godsend... lol. Also, the Wii version of Pikmin 2 was released for $19.99 MSRP, so getting a new copy for $20 shouldn't be a difficult process.
Also, a minor nitpick, but I find the packaging for the Wii version to be so much more beautiful than the Gamecube packaging.
Pikmin 2: Gamecube Edition (Wow, less than $30 for a used copy is a godsend now... used to go for above MSRP)
Pikmin 2 Nintendo SelectsSo, in conclusion, get Pikmin 1 on Gamecube, and Pikmin 2 on Wii. The fact that the Wii version of Pikmin 2 will be playable on Wii-U is a definite bonus, and a good way to get accustomed to what will be the control scheme for Pikmin 3(It's the reason why I got the Wii version despite owning the Gamecube version)