The Wiicraft thing seems cool (might give it a try), as that's how I'd have it set up (mostly button controls), but this doesn't allow for use of the motion sensors.
I'd have it set up so that to run you wave both the wii controller and nunchuck up and down (like your hands would move if actually running ... the longer you can do it, the longer you run for in game. Fighting would also use motion controls - allowing you to attack / block quickly and easily.
Now ... where did I put my Bluetooth dongle?