The Wii U controller did not always control similarly to 3DS.
Nintendo's Wii U controller originally utilized raised analog sticks rather than the Circle Pad made famous on 3DS, as reported in recently unearthed documents published by a NeoGAF user.
The diagrams show the original with a nearly identical design (though some ports and the stylus had slightly different placement), but the analog stick was raised. What led to this decision is unknown, as well as whether the leaked images (which were given no definitive source) are even legitimate.