I haven't played OoT on Wii U, but I have the exact same problems you listed with Donkey Kong 64. I still like it enough to keep playing it, but man, the controls can get frustrating. Some of mini-games that require precise movements make me want to throw my controller at the wall. Also getting pretty sick of using my instrument instead of getting long-range weapon out. x.x
Basically, it seems like the controller is the big issue. Not sure about the joystick controls themselves, but lack of C-buttons on the Gamepad/Pro controller means you'd probably have to use the right joystick. Maybe using a Gamecube controller adapter or being creative with how you map buttons might solve it...but it's still definitely a problem.
NNID: Zephyr25 / PSN: Zephyr--25 / Switch: SW-4450-3680-7334
