I actually feel Yveltal has had a more positive reaction than Xerneus (though both are immensely popular). X will inevitably sell better because X is a "cool" letter. I'm undecided, myself. I'll weigh all the differences. Right now the score is 2-0 in favor of X because I like Xerneus slightly more than Yveltal (though Sugimori draws Yveltal better than Xerneus, the concept art is way better) and blue is my favorite color.
In terms of the boards themselves, as others have said, it's simply because the "Red" version of the game always has the more active board. People post on the HeartGold board more than the SoulSilver board even though SoulSilver sold more copies I believe.
Well, my favorite color is blue, so that's a factor. I'm a really big fan of deer, and base a lot of things around stags and wolves. Though I think Xerneas may be female due to, well, X, plus female reindeer also have antlers (and if Xerneas represents the north pole with Yvelta representing the equator as I'm guessing, it would stand to reason that Xerneas was a feminine reindeer. Even though they'll probably be genderless.
But it doesn't matter since I'll be getting both anyway and I prefer blue.
"The point of war is not to die for your country. It's to make the enemy die for his."