Some changes have been made to the Wii U Controller as revealed in previous posts and in the Nintendo Direct conference, including the Wii U Controller Card Reader/Writer NFC pad, and the Wii U Controller Dual Control Thumbsticks.
The back of the controller has been made more comfortable to hold, and the button layout has been slightly changed. You can also now use the Wii U Controller TV Remote feature, which is also HUGE and a first from a videogame device.
Also confirmed is that the Wii U GamePad will have motion control support via a built-in Motion Sensor and Gyroscope, which will allow you to tilt and move the controller to control the action in the games. This is not a new feature as it appears in the 3DS and in a lot of current devices, but its good to have it confirmed!
Skip to 8:44 into the Nintendo Direct E3 2012 Pre-E3 Conference video to see Satoru Iwata discussing the new motion control gyro and motion sensors built into the Wii U Remote!