I prefer using the GC controller, and I don't change anything except for turning tap jump off.
Tangentially: As for which shield button I actually use, though, it's R (shoulder). I just don't understand how using L is comfortable for right-handers. If I use L to shield, I feel like I might throw off my character's movement sometimes, just due to having to apply pressure to an area near the control stick. I also use X to jump instead of Y, but I'm not sure if that's unusual. By the way, I'm a right-hander and I clap with my left hand ontop. Just putting that out there. I seem to be slightly abnormal.
Now, when it comes to the standard button layout (Joy Con and Pro controller in my case), I take heavy influence from the Bleach DS fighting games, in which Y, X, and A were attack buttons, and A was used in combination with a direction to grab. And for jumping, SNES Mario game influence.
Y: Normal attacks
X: Special attacks
B: Jump
A: Grab
C-stick? Don't use it.
Everything else (save for tap jump) is default, I think.
It just bugs me that I have to swap names on my character if I switch controllers. I haven't looked in the records yet, but I assume it's like it was in the past, where stats are tracked by player name. If not, my memory is off -- I haven't been fully absorbed by Smash since Melee, so I haven't been paying as much attention to the minutiae in the games since.