I would go with a 3.o spec motherboard and a 2.0 card for now. Early benchmarks say the the new 3.0 cards are not a huge improvement. Just get the highest end 2.0 card you can, and then upgrade when it gets to slow, or as newer 3.0 cards get fast enough to make the upgrade worthwhile. At least you'll already be set up on the motherboard.
Your budget is $1000-$1200? Too much... I guess you put another dollar not USD.
You can get a 6970 (which is when you like ATi/AMD) or a 570 (nVidia), then skip kepler or 78xx. Because we don't know them yet and maybe it's disappointing. Who knows? We do better buy now and buy the generation after the Kepler and 8xxx series or anytime where your cards get slow at gaming standards.
PCI-E 2.0 and PCI-E 3.0 shows very little performance difference in 7970. In 78xx or kepler it should be the same, so you are OK with a PCI-E 2.0 Motherboard. But maybe PCI-E will be more future proof. It's really going to depend on you really.
I agree with refillable, get the 6970 now and when the 89xx series comes out or Nvidia equivalent arrives look into getting a 79xx series by then the cards will be fully tested performance wise and you'll have a better idea what your buying. the 69xx or 5xx series will max out most games for years to come anyway, and you'll save some cash
As someone who has been building for 24 years, I have to say that the bleeding edge ain't what it use to be. The increases these days are so slight that they are just not worth the money. In this case, based on the current 7900 series cards that are out, there is no reason to believe that the 7800 series will be any great improvement either. However, the PCIe 3.0 motherboard will set you up for future upgrades at relatively little extra cost.