The answer to your question depends on the cpu you are using. Sandy Bridge (2000) series cpu's only support pci-e 2.0 because of their built in controller, so getting a new motherboard with a pci-e 3.0 slot will not make a difference. Now if you are using Ivy Bridge (3000) series, then yes getting a new motherboard will allow you take advantage of Ivy's pci-e 3.0 controller.
You will not notice a substantial hit in performance using pci-e 2.0, I would recommend waiting and updating your system to either Haswell or Broadwell cpu. You will be able to extract more substantial performance from your system then.