Wind Waker was never the best Zelda game anyway, I always thought it got too much praise just for being Zelda. Still better than most of it's type, just not as great as the hype.
As for the controller, it's not the best of course, purely down to size. But the point being it wasn't made to be a standard controller and what it does, it does very well. As for fps type games, well there's not a lot to test, but Zombie U is a really good game and works brilliantly with the controller you should try that.
Mario Kart 8, Splatoon, 3D world (though I'm not it's hugest fan), Zombie U and a few others aside, the games are where this fell short. Sadly