Agree, Gamepad should be first-intent, but with as much functionality as possible. Maps, UI, inventory etc. Maybe the motion controls could be for flying/swimming/driving/projectile weapons? There really aren't many games that have made any use of it whatsoever, other than being a secondary platform for when someone else wants to use the TV. I think Nintendo made it very difficult for themselves trying to design for 2 screens when players only have one pair of eyes, so will only ever be able to look at one screen at time.
So, maybe that's the trick, for Project Ukulele to use the screens in conjunction with one another, instead of separately. Like, what if a character needed to see something far away, so they could hold up the Gamepad, parallel to the TV screen, then move it forward and back to zoom in and out, up and down etc? Or for targeting long-range weapons, sniper-style. Or inspecting things at close range, like a magnifying glass, looking for clues to find pagies. There's got to be a mini-game in that, somehow.