I'm still debating this one, but I wanted to give every one an update on my current research so that people can discuss and possibly learn something new.
1) If I go to Intel I feel I will have to go with an i7 or something in an 1150 socket. As much as the 1155 socket is powerful and established, the upgrade path for 1155 is fizzling out. If I am throwing down some bones now I want to make sure that throw down smaller bones later.
2) The newest cards are PCIe 3.0, but you can run them just fine on PCIe 2.0 slots. Optimally you would want to run them on 2 slots of 2.0 @ x16. Due to how PCIe is done this is equivalent to two slots of PCIe 3.0 @ x8. That's not a complete comparison, but it's close enough for the considerations of video cards. You can, reportedly but not demonstrated, go as low as PCIe 2.0 @ x8 and not see any hiccups.
3) If the future of PCIe 3.0 is something you are concerned about then know that for AMD processors you will currently need a socket FM2 board and processor. The AM3+ socket doesn't support PCIe 3.0.
And after all of this.... I still have no idea what I want to do yet. It certainly is nice to use parts I already have and keep going the AMD route, but if I change over I have a decent upgrade path and can use my old hardware as a NAS box.