Usually I pick my version based on whatever version mascot I like more (Blastoise, Ho-Oh, Groudon, Palkia...)
The problem with that system is in a LOT of cases, the version I don't pick has all the Pokemon that I really like as version exclusives (couldn't get Electrabuzz, or Phanpy, or Delibird, or Lotad, or Sableye, or Honchkrow, or etc. etc.)
So with Gen 5 I mixed it up and I didn't make my decision based on the version mascot I liked better, but by the exclusive Pokemon available in it (I got Black despite liking Zekrom more so I could catch Vullaby and Gothirita and such)
Since we don't know any of the exclusives yet, right now I will be getting X because I really like Xerneas.
But if Y ends up having more exclusive Pokemon that I want to use in it, I'll probably switch over.
Don't forget to check out my MegaTen themed webcomics at http://www.drunkduck.com/user/Strain42/ (Currently Updating: Persona 4TW Add-On M-F)