The 3DS would make a terrible gamepad, just like the Vita does. Both devices lack buttons and the workarounds are aweful.
Doesn't this add all the missing buttons?
And its still missing clickable thumb sticks. I just don't see why they would implement the 3DS to function as a controller when the UPad, which comes with the console, does EVERYTHING the 3DS does and more and in a higher quality. The Vita adds something to the conventional PS3 control scheme so it kinda makes sense for certain games but there's really no reason to implement the 3DS in a similar fashion.
Just so you can use it as another Upad? People still have Classic Controllers (and Classic Controllers Pro) and I'm sure Nintendo will find some way to implement them with alternate control schemes, even with the WiiU Pro controller being available... It doesn't seem impossible to use the 3DS, especially the 3DS XL, with a circle pad (or the Nyko version) as a Upad, minus the clicking sticks...
Another option is to use the 3DS w/ the circle-pad add-on instead of using a WiiU Pro controller, mapping the Left and right stick-clicks to the touch screen...
It might not happen, in fact, considering the 3DS's battery life isn't the greatest, I would have to say it's unlikely, but it is possible and reasonable for people to want. not to mention it would be another plus to buying a 3DS and/or Circle pad Guitar Hero 5 allowed peple to use their DSi's to play in the game, iirc.