An image published to Twitter, and since taken down, by a QA tester for LEGO developer Traveler's Tales, depicts a WIi U controller with traditional twin analog joysticks, not analog pads similar to the 3DS', as had been shown in earlier images of the controller.
Games Radar, which first reported the picture, notes that the start and select buttons have shifted, as well as the existence of some new square button on the left side whose purpose is unknown. This controller also carries the Wii U branding, unlike previous models.
Development kits may differ from the actual consumer product, of course, though it would be unusual for developers to get a controller with proper analog sticks if the commercial unit still featured the nubs. It may also be a future or alternate model that won't be released at launch or be available separately (which would be a publicity disaster for Nintendo.)
Everything is conjecture at this point, but again, I've asked a Nintendo of America representative if the company wishes to address this variance. Guess we'll find out more at E3. [Update] As expected, the NOA representative said the company does not comment on rumor or speculation.