Yeah, we could see a more scientific, genetic altering team with X and Y. I think X and Y either represents:
The axes on a graph, or the chromosomes that distinguish boys (XX) from girls (XY). I've been thinking about this too, and it would even be cool if we could see an evil group return like Team Rocket. Nevertheless, I hope the evil group is more scientific as well.
Pokémon X and Pokémon Y probably represents the chromosomes or it could possibly mean width and height. The team could be called Team Genetic, seeing as the games seem like they'd have a story about genetic kind of stuff.
Either way, it sounds like it's going to have a great storyline to it.
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I myself, am leaning more towards the possibility that these games can represent biology in general, but, as I came to learning more and more about these games, a lot of people have quite interesting theories! Like in a thread I made about Dimensions in space, maybe x & y can represent the 3D axis, which can correspond with dimensions, or in mathematics in some way.
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The natural pokémon vs. manufactured pokémon theory is very interesting (not to mention topical, with humans likely to bond themselves closer and closer to computers as the years go on). I think it has absolutely tonnes of potential. The evil team could believe that natural pokémon are so last year or whatever. I had an idea where Yveltal was a formerly natural pokémon that the evil team mechanized and you use Xerneas to save it but obviously that can't happen with both legends being exclusive to one version.
Still, an evil team who thinks the only way for the human race to advance is to create their own pokémon has lots of potential. I'll be disappointed if the story doesn't at least partly revolve around that, now.