I was initially unimpressed by the motion controls, and in fact was unexcited about playing the game because both control options just didn't work for me. However, on my fourth or fifth day, the motion controls finally made sense. Now I think they're some of the best console shooter controls I've ever experienced.
The major change I made was to SLOW DOWN (when getting adjusted to them, now I'm blazing through the maps). Really focus on aiming in the general direction you want with the right stick while keeping your hands steady on the motion controls, and only after you're looking where you want, gently move the controller down and up to cover the map or to aim at an enemy. You don't want to learn by using the stick and motion controls at the same time like a regular dual analog game because it will fuck you up.
Once your mind separates the two functions it will click. And when it clicks, it will be glorious.