I still haven't found a control scheme that makes me happy with Pikmin 3
I like the way Wii Motion+ & Nunchuk, but it wants me to use Gamepad for pause-menu interactions and that makes me really dislike the games controls.
I also dislike the dual-analog / gamepad only controls. The new stylus/touch based controls not much better. All I want is to play the game without being forced to use the Gamepad, but they don't provide that option.