A QA Tester from TT Games, makers of the LEGO series of games, recently posted on Twitter a picture of a newly designed Wii U controller. Soon after, the Twitter account that posted the picture has since been deleted.
As you can see from the picture above, the most noticeable difference between this new model and the one shown at E3 are the use of raised analog sticks, instead of the 3DS-like circle pads. There are also a few arrangements of other pieces, like the plus and minus buttons appearing under the face buttons. There's also the placement of the Wii U logo on the controller, perhaps indicating that Wii U might be the console's final name.
This controller could most likely be from a dev kit, and not entirely represent what the final design of the Wii U controller will be. It's also quite similar to an earlier design concept of the Wii U controller.
E3 2012 is just a couple weeks away, so we'll find out soon just what the final design choices of the Wii U become.
Source: GoNintendo, NeoGAF