The Wii U was stuck working against itself in a number of ways. On paper, the idea of bringing the DS's successful format to a console sounded great... but couldn't actually work the same way in practice.
The first problem was that human eyes can't focus on two screens at different distances from the eye. You can't actually look at both screens together, you have to switch your focus from one to the other.
Then there's just the economic reality of console development requiring developers to prioritize multiplatform development. No one wants to design a game around the Wii U and have it be exclusive to the Wii U. That was viable for the DS because the DS was such a massive juggernaut, and because handheld titles could be developed on a much smaller budget, but Wii U exclusivity could never be justified. Games that are being developed for other single-screen platforms and then ported to Wii U can't do much with the Gamepad.
But perhaps the most ironic nail in the coffin was that the best use case for the Gamepad, Off-TV Play, could only be supported by games designed around a single screen. Developers shouldn't make the second screen important or else they lose this feature!
But the other two did get ported to Wii under the title Metroid Prime Trilogy.