I was hoping the reason was more like "We've abandoned the touchscreen controls because they were complete garbage and the only reason anyone would choose to make a game control like that is if they felt internal pressure to push a controller gimmick that they talked up big and then struggled to make good use of."
While it's nice for 3D to "save" Nintendo from themselves in this case, 3D is also a dumb shallow gimmick so I don't really like how it is dictating controls either, even if in this case they happen to be in my favour. I long await the day when Nintendo does a complete turnaround on these dumb gimmicks. They've either run out of ideas or do not truly wish to be creative anymore and the gimmicks exist to create the illusion of innovation when we're really playing the same cookie-cutter bullshit over and over again but with some shallow hardware gimmick forced into it. I honestly believe Nintendo will never be truly creative again until they ditch the gimmicks and cannot pretend that a game is new and different because it has wacky controls.
Since Nintendo did not state that touchscreen controls suck, but just that they don't work with 3D, we cannot be certain that they won't use that garbage in a Wii U Zelda. The Gamepad just begs for shitty touchscreen controls.