On a computer, it kind of disrupts the smooth flow of the game when I have to use the mouse to click the "Yes" button with precision(Yes, I'm plain lazy, but isn't that what the world's becoming as well with tech advancements?).
I just feel that it really makes gameplay more fluid when you can press Z or Enter facing water, and then press it again to accept the Surf request etc.
This can be applied to more than Surf, such as headbutt or dig, and using the keyboard assignments to choose the Pokemon from there.