Well currently, the controllers are built on to the board. However even the highest end radeon 7970 can't fully utilize (saturate) the older pcie 2.0 slot. Just pick up a z68 board with pcie 3.0 and wait a few years until we actually get cards that can fully use the pcie 3.0 slot.
I do understand the practical side of PCIe 3.0; I was just trying to ask more about the workings under the hood. What is the purpose of the controller chips, and why, if they're built onto the board, are they dependent on the CPU?