I believe the thermal pads are grossly inefficient in heat transfer. Paste is a very thin layer, only filling the near-microscopic irregularities in the metal of the CPU and the heatsink and for the rest allowing metal-metal contact which is very efficient in thermal transfer. Pads are only good for passive heatsinks that does not have the pressure that can be put on the CPU with the cooler backplate.
Edit: Also, pads are good for things that don't generate as much heat as a CPU or the chip on the GPU. - VRMs and memory. Paste for the really high generators of heat that require efficient cooling and heat conducting.