IIRC, Intel wasn't able to get PCIe 3.0 working/validated in time for the x79/ LGA 2011 launch. The thing that saved them is that SB-E processors have a rediculus amount
of PCIe graphics lanes ( 40 ) and even the AMD 7970 Ghz edition can't fully saturate 16 lanes of PCIe 2.0. Having PCIe 3.0 makes a much bigger impact in IVB since they only have 16 lanes of PCIe 3.0
(=32 lanes of PCIe2.0). In summary, I wouldn't worry too much about it at this point.
Main: i5-3570K, ASRock Z77 Pro4-M, MSI RX480 8G, 500GB Crucial BX100, 2 TB Samsung EcoGreen F4, 16GB 1600MHz G.Skill @1.25V, EVGA 550-G2, Silverstone PS07B
HTPC: A8-5600K, MSI FM2-A75IA-E53, 4TB Seagate SSHD, 8GB 1866MHz G.Skill, Crosley D-25 Case Mod