Go for it.
I know that I am very happy having switched my main system, to a 2500k Intel rig from AMD.
Personally I don't think you need to get too hung up on whether the board has PCIe 2.0 or 3.0 as early indications are that it really doesn't make that much difference. Of course, as other hardware and their drivers catch up then this could change.
If you are thinking of building in a little future proofing then go for PCIe 3.0 and wait for the new chips to come along and this might fit better with your budget and plans to put the new rig together.