I'll have both at some point, but the one I'm getting first is Omega Ruby. I like Groudon a little more than Kyogre, plus I plan to bring an Oshawott from Pokemon Bank to be my designated water type. Plus, I always go for the first in the version duo Red, Gold, Ruby, Diamond(though I actually got Platinum), Black, Black 2, X, you get the drill.
All that being said, it really does not matter much in the end. Unless you vastly prefer the version mascot, or version exclusive Pokemon, it rarely makes a difference which version you choose.