What's wrong with the shoulder buttons? I think I can guess why based on my own experiences, but I'm curious to know why.
What Equinox Fox said I agree with, the buttons feel dull physically, but in terms of mapping I keep tripping up over which button does what. I want to use L for shield/rolling and r as the grab, and I'm pretty sure that's because in my head I've designated my left hand for movements and my right for attacks. That complaint falls under something that I'll just have to get used to, but I wonder why it is that way by default since the GCN controller has Z as grab on the right side which always resulted in my using L exclusively for the shield.
I agree with Raptor here. I am a "hardcore"(not really) smash player that only uses the GC controller and still, I found the controls for Smash 3ds to be very comfortable. There has never been an item pick up button and maybe that's why I don't find it annoying, but using the attack button to pick things up has never been a problem for me. I've never had a time where I was doing an incredible combo and then suddenly being interrupted by picking up an item, so honestly I don't see why you guys hate it so much. Picking up items with X or Y would've been very annoying in my opinion because instead of having my thumb rest on the attacks buttons I have to move it just to pick something up(trust me, this is WAY more annoying than it sounds). I only use the control-disk-thingie to jump because then I have much easier time playing and I don't get as tired. Maybe that's just me. I do get Equinox Fox's concern about the shoulder buttons though, they can be a bit annoying at times.
I haven't played All-Stars for the vita though, only on the PS3 and I liked the control there.(I didn't like the game in it's whole though. No bias, I just didn't like the mechanics and the "you have to super move to win" idea.)
Again, most of my gripes have to do with personal preference (aside from some awful framerate issues I was having). Although, I think it's a little ridiculous to support your preferences by saying you would get physically tired just because you're moving your thumb a few centimetres to another button. If that were really an issue I don't see how you would be able to play most other video games considering other games actually make full use of what buttons are available. You're still entitled to have them, don't get me wrong here, but if you're telling me my preferred controls wouldn't work for you specifically because of that then it's not very convincing. Not that I think you should be happy with what I want.
I think part of designing a game for handheld which is traditionally a console game should involve optimizing the controls for the format instead of sticking as close to the originals as possible. It doesn't work for me in this case because the positions are different and the 3DS doesn't have as many inputs. When I first posted this I wasn't aware that apparently the 3DS version lets you remap every button, so to be fair most of what I'm complaining about wont be a problem in the full version. That being said, I still think my complaints about the default controls are valid.