For all my research, the only "option" available is to go to the in-game controls menu, and switch the aiming reticle to buttons. Then, reconfigure the controls of the emulator to have each button mapped to the right stick.
Does that work? Only technically. The main problem being that the aiming reticle follows Pit's movements. You can't, for instance, move left and aim to the right side of the screen.
Besides that, Pit's ground movement is incredibly dodgy. If you move the left stick even slightly, he starts dodge rolling all over the place. Hardly controller-friendly IMO. Basically makes the game unplayable.
If there is a better method of control that I'm missing, I'd love to hear about it!