IMO the best way to aim a portal gun would be the way the laser is aimed on Super Geometry Dust.
Maybe the portal gun could be controlled by right nub for direction and L/R triggers for firing red/blue guns.
Then direction/run/jump could all be handled by the left nub. Pressing lightly on the nub would walk left/right, whereas pressing all the way left/right would cause mario to run left/right. Pressing the nub up could jump.