With Nintendo considering the prospect of making Wii U games that use more than one of the new controllers, it's apparently possible that we could even be using the 3DS as an additional controller too.
During E3 2011, Shigeru Miyamoto was asked by Switched On whether gamers would be able to use two of the touch pad Wii U controllers on the same console and his response suggested that even Nintendo wasn't quite sure:
Our basic premise is that you can use one [Wii U controller] with a system. If we got to an idea of having multiple [controllers] it might be just more convenient for people to use their Nintendo 3DS and have a way to connect that... That being said, we are doing research about if someone brings their controller to their friend's house and they want to play together on Wii U to whether or not something like that would be possible.
It sounds like the functionality of Wii U might not be finalised at this stage so it will be interesting to see what else regarding the console will be made public from now until its 2012 launch.