If you're unsure, then just go with the brand that you're most comfortable with. For example, with the 2 companies you listed, I'd just go with Asrock and find the board that fits your features and budget.
Help anyone!?! Asus X99 boards selling for 274.99 to 383.99, Asrock 215.99 to 283.99 and MSI $194.99 and up on Newegg, which one to choose?
http://promotions.newegg.com/asus/14-6721/index.html?icid=292039
http://promotions.newegg.com/mb/14-4664/index.html?icid=274730...
Z97 Extreme9 on Amazon: http://www.amazon.com/ASRock-EXTREME9-DDR3-Motherboards-Z97/dp/B00KZNUB74/ref=sr_1_1?ie=UTF8&qid=1417796042&sr=8-1&keywords=asrock+z97+extreme9
You can try a Gigabyte, Asus or Asrock if you want to avoid MSI, starts at just above $110 or so:
GIGABYTE GA-990FXA-UD3 - http://www.newegg.com/Product/Product.aspx?Item=N82E16813128514
ASRock Fatal1ty 990FX Killer -...
Between the EVGA and Asrock, definitely go with the latter. But I hear there are also Asus and Gigabyte that you might want to also take a closer look at.