PCI-E 3.0 is more of a gimmick like DDR4 ram than it is actually more useful than PCI-E 2.0. Unless you're packing 3X+ graphics cards you won't be needing PCI-E 3.0.
Personally go with whichever motherboard has either the most solid reviews or whichever one I want. Asus is a great company but their quality control is severely lacking sometimes. Gigabyte though always makes you pay for return shipping to their RMA facility and the RMA process COULD be lengthy.