I will most likely not be using SLI or Crossfire in the future. USB 3.0 header is nice. CPU will be an FX 6300. GPU will be a GTX 760 SC 2GB. I might overclock but I'm still not sure. Cooler I will be using will be a Cooler Master Hyper 212 EVO.
The M5A99FX PRO R2.0 is a better choice than both of those boards and it supports crossfire/sli configurations at pci-e 2.0 x8/x8. It also comes with more SATA and USB connections than the EVO board.
Pick whichever looks better in your build, although I heard the newest version of the ud3 was bad both should handle overclocks up to 4.6 and 4.8 if you get really lucky. I would get whichever is cheapest personally