There's a huge argument over on IGN's forums about this very subject (clickable sticks on the Wii U controller). It seems a few people don't have much imagination when it comes to alternative control schemes.
You don't need clicky sticks in a shooter. Plenty of shooters on the Wii played just fine, and in most cases, "run" was mapped to the A button.
The Wii U's touch screen will give developers more room for creating customizeable controls. You can use the screen to plan airstrikes, moving a cursor to the exact position of the target. You can use it to set mines around the map.
Here's a control scheme I thought of, and another poster on IGN had the same idea.
Left Circle Pad: Move
Right Circle Pad: Aim / camera movement
D-Pad: Weapon / grenade selection
L Trigger: Aim down sights / aim grenade trajectory
L Button: Throw grenade
R Trigger: Shoot
R Button: Melee / knife
A Button: Jump
B Button: Crouch / cover
X Button: Sprint
Y Button: Reload
Touch Screen: Direct airstrike target, place claymore mine, hotswap weapons