I see the touch screen being incorportated into a right-handed controller thumb area that also incorporates an analog stick. We are all use to our right hands controlling the majority of in-game actions so this makes the most sense.
The left side or left hand controller would be a more traditional layout with the addition of gyroscopes. Both controllers would contain gyroscopes, but the left-handed controller would be the primary means of controlling movement, while using the right-handed controller or both controllers together for movement would be secondary.
I see both left and right handed controllers containing sensors that track where the controllers are in relation to each other, to the Revolution, and to the controllers of other players. This allows players to perform complex actions with their arms including dance moves and player to player interaction.
Shaking, tilting, raising, lowering, swinging, extending your arms and such would be primary methods of interaction in Nintendo's titles.