Intel is a very careful company. They spent hundreds of millions of dollars replacing motherboards that might have had a slight degredation in quality on one peripheral after 3-5 years on a small number of boards. The Sandybridge-E have all the necessary equipment to run PCIe at third generation speeds (PCIe 3.0) but due to there being no third gen cards available to test it with when the Sandybridge-E and X79 chipset launched they only marketed it as being 2.0 capable and left it up to the motherboard manufacturers to decide whether or not they wanted to turn third gen speeds on.
I'm running one with third gen speeds right now, works great
There really is no use of PCIE 3.0 for gamers, so I wouldn't worry! Where PCIE 3.0 bandwith is needed is for maximum bandwith in programs such as Adobe After Effects, which can always use faster gpu accelelration! This is why Quadro cards when equiped with 3.0 later on can really shine!
PCIe lanes are interleaved so a fixed size dataset gets to the GPU quicker and thus it has to wait less than when running at second generation speeds. This is why most benchmarks show a marginal improvement when switching from second gen to third gen