PCIE 3.0 isn't the main reason. Usb 3.0 , data 6G, free ramdisk software, is. The newer platforms also run lower power, faster ram, the PCIE 1x lanes can support faster speeds for expansion cards (thunderbolt card for example), EUFI is amazing, the processors do have new instruction sets, as well as faster in single threaded applications.
Usb 3.0 on the black edition board is a lot slower, same with data 6g. The PCIE lanes aren't a big deal now, but 2 years down the road it might.
The cost difference is nearly identical right now.
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