The main reason I got used to the GameCube Controller primarily because of the analog triggers (the "clicky" L & R Buttons, which always make me feel nostalgic), along with the overall placement of the buttons. It was my go-to in Brawl, as I vastly preferred it to every other kind of controller setup, but once Smash 4 came out, I actually alternated between GameCube and Wii U Pro Controller.
I can see myself switching to the Switch Pro Controller because the controller is probably the most comfortable one Nintendo has ever produced, though my muscle memory is tied to the GameCube Controller, so it is a little bit of a struggle deciding on one in particular for Ultimate. I don't think it helps that I am planning to get both limited edition controllers, but it is entirely possible that I might switch to the Switch Pro Controller this time around (something I never considered before today honestly).