I also mainly use the 3-button controller, but when I start getting frustrated in parts with games in the future I may look into pulling out a 6-button if they're less clunky for precision stuff.
6 button for me
I love the 3 button controller. The d-pad is better than the SNES one (I like how easy it is to hit diagonals), and I like how big the controller and its buttons are. Way better than the 6 button, which I only use if it's absolutely necessary.