I only use the GameCube controller for Super Smash Bros. I've used it in every Super Smash Bros. game since Melee, so I'm just accustomed to it at this point.
I usually use the Joy-Cons to be honest, but just because I don’t have the money for a Switch Pro controller right now. I’m planning on using that money for Pokemon Sword.
The Pro controller. I usually go with whatever's the nicest for the game (the classic controller for Brawl and the Wii U Pro controller for Smash 4), that way it's easier to go back to older games. Each game and the characters in each game all play completely differently, so having a different controller to highlight those distinctions even more helps imo.
I couldn't see myself using a nearly 20 year old controller for the most modern game honestly.