Or they could just design controllers with more buttons. I mean, pick up a controller nearby. How many of your fingers are you actually using?
As for your mouse, it's not necessarily any more efficient than a D-stick. You have to move your entire hand around to make a mouse do what a D-stick can do with a thumb. I hardly call that efficient. The only difference is that D-sticks aren't optimized for the user interface in the MMOs. That's more a design issue for the developers than a problem with the peripheral.