Will PCI Express 3.0 make a difference ?

Not really

Not at all, the bandwidth on a 16x pcie2 slot is more than enough for any single card even 8x would only see a few frames difference if any at all .

The only time you would start seeing problems is if you was trying to run sli or crossfire and your second pcie slot was only at 4x

The pcie 3.0 at 4x still has enough bandwitdh at the moment for high end single and dual cards meaning the performance would be only slightly worse (in the lower single digit percentage)

http://www.hardocp.com/article/2012/07/18/pci_express_20_vs_30_gpu_gaming_performance_review/13#.VJNmK14hPE

The link above shows the games with the biggest differences many other games do not show such gains.

Hell, even pci-e 1.0 at 16x is only just recently starting to show its age with some of the new cards.

You are A-ok.

Here's a PCI-E comparison review done on techpowerup.com - should answer all your questions you may have about 3.0.