Felt the same for the 3DS version, and actually, I don't like A and B used as the smash and special attack buttons, so I moved those to B and Y respectively. Even on Wii U, despite the fact that I don't even use anything but the Gamecube controller. The main reason for switching the shoulder buttons on 3DS was because it didn't feel right; remember Smash 64, when guard was Z and R was grab? For that matter, every controller I was used to using for any Smash game had the grab button accessible via right hand: R on N64, Z on Gamecube controller, D-pad on Wiimote/Nunchuck... I never used a Wiimote alone for Brawl nor a Classic Controller, the latter of which I don't know their controls anyway. So yeah, definitely had to switch those on the 3DS version.