I don't know how cost effective certain technologies are and I don't know how small the chips have to be with the touchscreen, 3 camera's, motion and gyro sensors, 3D slider, buttons, 3DS/DS cart slot, SD card slot and slide pad.
What I do know is that to make tech smaller it also makes it more pricier. But most important of all. The resolution that the 3DS produces (400x240 & 320x240) is a lot smaller than the Wii can produce.