It really isn't. The face buttons resist being pressed a little too much, but overall it's still decent.
There are basically two schools of controllers, and people have some trouble crossing over:
1)Grip it by the horns. These are meant to be held tight with firmly closed pinky/ring finger and sometimes middle finger. The palms/base of the thumb always touches the plastic. If you relax your thumbs, they'll both be pointing directly away from you, almost parallel to each other and parallel to the controller's top surface.
2)Free breathing. You balance them on just the tips of your pinkies and ring fingers but the rest your supporting fingers or even the palm don't touch the controller. Your wrists will be further away to the side and higher than the controller's base, and your relaxed thumbs will point inwards, coming down onto the surface only with the tips and first joints.
Prominent members of school 1 are the N64, Gamecube and Xbox pads. The DS tank feels like this, though it lacks the horns (you just grip it very firmly).
Prominent members of school 2 are the NES, SNES and Playstation pads and the Classic Controller, and probably this new one. The DSlite and PSP work like this as well.
If you treat a school 2 pad like a school 1 pad, dicomfort and cramps will be the certain result. That doesn't make them bad. You're just approaching them wrong.