The layout isn't as smooth for pushing the 5 buttons required and 2 control sticks as smoothly as a traditional controller. If they use the touch screen, it probably won't be as fast. Plus, it would be awkward to be pushing the buttons on the screen at a frantic pace. I would be afraid of breaking it!
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The real reason is it's not as easy to get to each button.
But the button layout is what defined fighting games since the SNES up until now. I love the Gamecube layout but the rest of the industry did not and stuck with Nintendo's diamond shaped buttons of 4. You have Jump, Attack, and Special Attack, and it's set up more like the N64 which was perfectly fine. Then you have the 2 sets of shoulder buttons in a much better position than that awkward Z button ever was.There really is nothing wrong with the button and stick layout as all the traditional fighters have been using that method on home consoles since Nintendo invented it and up to this very day.
The positioning of the buttons compared to the stick is actually in the perfect position, just flipped from the C Stick way. Maybe you are thinking about the Wiimote trying to use the A button, and the D Pad, and the lower 1 and 2 buttons, now that was awkward. This controller literally is the undustry standard with a screen in the middle. I can guarantee you moving your fingers at a proper speed will not be an issue.
As for the screen, all we need is Sakurai's take on the whole motion craze to see that Smash is going to be as traditional as ever. He added motion with the wiimote for people who wanted it, but it was hardly a focus and barely anyone ever went that route, especially in the hard core tourny scene, you specifically have nothing to worry about. Now there very well may be instant smash attacks on the screen, much like SF did for their big moves, but it will be no different from C-Sticking and not to mention if the extra stick is faster, you can bet the screen will be largely ignored.
Fighting games in general just don't lend themselves to well to the touch screens, and so far the DS and 3DS proves it. Options are there, but they have never once broken the game. Smash will be smash and you can bet on it.
Only thing the controller will do for is, is make things so much more convenient with our social networking, setting up matches and such.
As for breaking it, If you've never broken a ds, your phone, or ipad by tapping it, chances are you won't break this. It's Nintendo for crying out loud, if you can break it like that you deserve a medal.