While GPU's still cannot fully utilize the bandwidth of 2.0 currently, there are advantages to motherboards finally implementing a 2.1 or 3.0 interface. First and foremost, the power capabilities of 2.1 and 3.0 are twice that of 2.0. Either of the newer standards can provide 150W of power to the card through the PCIe slot interface itself. That means fewer and fewer cards would actually require a 6-pin PCIe power cable, and no card would require two such connectors (or a single 8-pin along with an additional 6-pin).
Also, a faster interface would provide more bandwidth for newer dual-gpu cards, which tend to under-perform compared to comparable SLI or Crossfire configurations due to having to be down-clocked for thermal reasons, but also because such cards can't always communicate through the PCIe bus itself fast enough. It could potentially eliminate the need for SLI and Crossfire cables, as well as on-board data transfer circuitry if the cards can simply use the bus itself to communicate.
Really, there's no downside with a progression to 3.0.