There's really nothing they can add to the controller.
I mean, it has everything, even NFC.
Secrets will come in the form of the online infrastructure on the system.
They could add a camera or sensor bar on the back to interact with the Wii U, Wii U's sensor bar, or a second controller and add depth, windowed views, or head/controller tracking.
They could add vitality sensing or touch sensitive input/sensors on the back to add immersive gameplay, heart rate monitoring, touch control, etc.
They could add eye/face tracking to see where the player (via the controller) and/or casual viewers (via the console/"sensor" camera) are looking.
They could add function without the console for download only or low CPU use games like casual games or functions for browsing while at McDonald's.
They could add wireless connectivity to other controllers/accessories.
They could change the screen to 3D like the 3DS or a pseudo 3D view while using a TV.
While not adding anything new they could explain:
The use of tilt sensing.
The magnetic sensing.
Third party software like Skype, TV, Internet, etc.
I doubt most of or even any of this will happen, but this is the speculation thread.