it will be fine. current top of the line cards (GTX 580 and hd 6970, even when overclocked to all hell) don't seem to suffer when you put them in an 8x PCI Express 2.1 slot. in other words, no performance hit compared to x16 pci e 2.1 slot.
kepler promises twice "performance per watt," which basically means that there wont be a crazy jump in performance. jest less power consumption and heat. i would think 15%, at best. same thing goes for AMD cards.
A PCI E 2.1 slot running at x16 will be fine. unless you are planning to shoot for their next dual GPU cards. in which case the cost of the mobo will be the LEAST of your concerns.