The group says otherwise:
http://www.pcisig.com/news_room/faqs/pcie3.0_faq/
They suggest it will be backwards compatible.
If you are buying a MB today, you will have a 2.0 or 2.1, and you will be able to upgrade the video card for many many years to come.
If you are buying a video card today, how long do you expect to keep your MB?
Many of the changes are theoretical improvements. For example, when the AGP/PCI express 1.0 changeover happened, in theory the PCIexpress had a theoretical speed bump since it had twice the bandwidth. But in testing many PCIExpress cards, with the same GPU, were actually slightly slower.
James