I use the Wiimote + Nunchuk, just cause it feels so much more ergonomical for some reason. However, as one person said, in order to use many AT's, you need the C-Stick, or a C-Stick equivalent. The only (practical, so not including like remapping the entire control scheme) options are; the D-pad, and shake smash. Neither of these feel ergonomical in the least, and thus it kinda destroys the only thing I originally found beneficial when using the Wiimote + Nunchuk. Things like DACUS, FF'less Dair's, and other various AT's make me regret my original choice. The only things I find the Wiimote + Nunchuk has over the GC controller are
1. Wireless (Controller -> Console)
2. Feels more natural (to hold; I mean you just have so much more freedom since your hands are seperate)
Now, the wireless thing is a big one, yet you can always buy a wavebird. (Do they even make those anymore?). I despise sitting like 5 feet from the screen, since my Wii is positioned up on this stand, and so I can't go very far without pulling it down, but, the wavebird is a sufficient solution. And as far a feeling better to hold, well, the whole D-Pad C-Stick thing, plus the taunt buttons, and the shaky (pun intended) Shake smash feature just completely counter this for me.
So, in conclusion, I wish I had bought a wavebird with smash. =/.