During the flight mode the stylus was amazing, but for the Land Battle I prefered the control setup listed above...
There are many different things to tweak:
Control Configuration
Step 1 - Choose how to move Pit (Circle Pad or ABXY)
Step 2 - Choose how to move the reticule (Touch Screen, D-Pad, Circle Pad)
Step 3 - The following six options can be switched around (L, R, four D-Pad directions): Align Camera, Attack, Select Powers (scrolling left), Select Powers (scrolling right), Change View, Use Power
Reticule / Camera
You can independently change the speed at which the reticule can be moved horizontally and vertically, as well as change how quickly or slowly the reticule stops moving after it's been flicked across the screen. This can be done for the Land Battle mode alone, the Air Battle alone, or both. So you can indeed tweak both modes separately! You can also invert the reticule movement either horiz or vert, or both at the same time, and the same goes for Pit's movements (on-screen arrows on the touch-screen show the changes to avoid any confusion).
More Controls
There is the option to turn off guide arrows on the ground, switch off homing shots, turn on an aim assist that guides the reticule automatically towards enemies in the Land Battle sections, and even an auto-fire function that fires whenever the reticule moves over an enemy.