Our tests showed a clear result: on only one game (Dying Light) there was a significant performance gain by using PCI Express 3.0 instead of PCI Express 2.0. Even at it, the improvement was of only 7%. On the other hand, when we used the PCI Express 3.0 x4 slot, there was a loss of performance on most of the games.
Remember that we used a high-end video card, in a high-end system. Even we had not run tests on a more basic system, it is logical to think that, on a system with a lower video card performance, the impact of the bandwidth between the CPU and the GPU should be even smaller.
So, if you are looking for a video card, CPU or motherboard to buy, the presence or absence of the PCI Express 3.0 connection should not be a crucial factor do decide what to buy, at least on a single-GPU system.