I'm more concerned with how the cover of the game looks than the different pokemon in each. Everything from the way the disc looks every day I put it in, to the icon on my 3DS when I select it, and the game intro that I mash "A" through every time. I want to see a soothing blue and a mysterious deer, not an eyecatching red with a dark bird on it. Might seem insignificant, but these things can make or break my mood whenever I start up my game.
And so although I like Y's common pokemon more, I'm still choosing X for Xerneas.