Personally, I find that the controls work just fine. You just can't play it like Uncharted 3 or Gears of War (just throwing in another 3rd person shooter) as the sticks are too small for that kind of accuracy. I find that it's easier to just get my sites up (aim) in the general direction of the enemy and then use the sixaxis sensors to actually line up/fine tune the shot. Using only sticks or only the sensors makes shooting unnessesarily difficult.
Coming from someone who is loves and plays a lot of 3rd person shooters (I'm a hardcore Gears of War 3 player), once you understand exactly how the aiming and cover systems work and work best, the game plays and feels much smoother.
Try the Unit 13 demo.