Wii U's controller will come with a built-in rechargeable battery, so naturally Nintendo will provide a means of charging it with the console. It may not be as boring as a cable though: it could be an immensely exciting cradle.
NeoGAF user Aostia claims to have unearthed a patent showing off a charging dock for the controller, which would work rather like the cradle included with the 3DS console. It makes sense: this close-up of the controller's bottom edge, taken from Nintendo's E3 photos last year, shows two metal contacts that would fit with a dock:
It's not so certain how the dock is powered, though we'd guess USB via the console. Expect mains charging adaptors to be very popular with third party peripheral manufacturers, though.