Number of PCIe long slots and difference in transfer speed of the lanes are really the only major differences it seems.
PCI Express 2.0 x16 >> 4 (x16, x16, x4, x4) >> ASUS M5A99FX PRO R2.0 = Of course if going to use dual video cards
this would be the better board. Otherwise about the same board as the other.
PCI Express 2.0 x16 >> 2 (1@x16 or dual x8) 1 (x4 mode, black) >> ASUS M5A99X EVO R2.0
The M5A99X EVO R2.0 seems no longer at the Asus site in their current mobo lineup. Some are still available at the seliing sites of course.
Either of these boards may run out of ooomph if one wanted to "really" push even just a 6 core processor. I would guesstimate somewhere in the 4.5Ghz range max overlcock, give or take a 100Mhz or so and depending on how 'good' the cooling of the cpu is going to be in the system.
RGone...