First, all the parts would be 3D printed, not just painted. Paint wears off and then looks ugly.
It would have a smooth black shell, both sides, with a shine on the front above the start button. All buttons/triggers would be made of that diffused clear plastic stuff (like this, but less transparent), because inside there would be LEDs that were programmable to be any color and any pattern. No labels on the buttons (e.g. the A button does not have an A on it. It is just blank). The two shells would be printed a little bit differently than the default controller shells are, to allow for a clear diffused plastic strip (like the buttons/triggers) to run along the center like this that would light up with the face buttons/triggers.
There would be no rumble pack (I hate rumble). Inside would be a Wii U adapter among other stuff (likely an Arduino [and obviously LEDs]).
The cord would be a bit larger to accommodate both cables, but not too much. The case would be braided like this, not rubber. It would also be significantly longer than the first gen cords. At the end of the cord there would be two ports, one GC and one USB.
No functionality changes.