You're looking for indies with good Gamepad support? Not including off-screen Gamepad play, here are some:
* Affordable Space Adventures (first grade gamepad showpiece)
* Runbow (ColourMaster and Grey Man)
* Year Walk (puzzle completely redesigned for gamepad)
* Stealth Inc. 2 (Wii U-exclusive asymmetric two-screen co-op mode and level editor)
* Swords and Soldiers II (touch UI, two-screen multiplayer)
* Nihilumbra (asymmetric co-op, touch UI)
* Tengami (fully touch-controlled)
* Stick it to the Man (mind-reading via motion control)
+
Spin the Bottle: Bumpie's Party (unique party games that don't need TV)
Trine Enhanced Edition (touch UI)
Trine 2: Director's Cut (touch UI)
Temple of Yog (world shifts between both screens)
Cubemen 2 (touch UI/controls)
Terraria (touch UI, long distance mining -coming soon, opinion based on 3DS ver.)
Human Resource Machine (fully touch-controlled)
Little Inferno (fully touch-controlled)
Castlestorm (touch UI/controls, two-screen multiplayer)
Squids Odyssey (fully touch-controlled)
Typoman (touch controls)
Canvaleon (paint camouflage)
Zombie Defense (fully touch-controlled)
Starwhal (Wii U exclusive asymmetric 5-player mode)
added a few that are more than just 1:1 multiplatform ports or use the second screen for more than just a map-like screen.