Even so, this is definitely welcome news, it means that the Wii U Controller will feel much more comfortable and more like an actual videogame console controller rather than a handheld.
If you are wondering what the difference is, play a game on Wii and use the stick, or on Xbox 360 or PS3, and then play on the 3DS and use the 3DS’ “Circle Pad”. That is what Nintendo was going to include on the Wii U controller instead of standard thumbsticks. Thankfully they changed their minds! Additionally, both sticks can now be pressed-in and clicked, adding two additional buttons to the controller! This is something that the Wii lacked, but the PS3 and Xbox 360 have always had. The PS2 controller was the first to have clickable control sticks. You can also see how Nintendo slightly changed the button layout and made the controller more comfortable overall.
This video shows off the new Wii U Controller Sticks at 5:33 into the Nintendo Direct E3 2012 Pre-E3 Conference video.