I felt like later in the Wii U's life, they were pushing it more as being for off-TV play, and that meant that that kind of stuff would have to be implemented anyway— Wind Waker HD certainly had the dual approach, where the default was to play on the TV with inventory on the gamepad, but if you played in off-TV mode, then the inventory was a pause menu popup. That extra development work to support both was probably invisible to most users who only ever played on-TV.

That combined with the increasing inevitability that everything was going to be ported to a later, single-screen system anyway, and it's not hard to see why titles like Donkey Kong Tropical Freeze and Zelda BOTW didn't use the secondary screen at all.