Yay, that's going to be a problem with the titles. Though anyone with common sense that no matter what Pokemon they make version exclusive or what past Generation Pokemon they make available to capture in the game, being Pokemon had had a small "racial" problem (via the above mentioned Jynx), they might be more careful to choose which Pokemon goes into what games (though this probably isn't even a big problem as long as they don't make any "stereotypical" Pokemon.
Only problem with that is what types will the "good" Pokemon be and also the "evil" Pokemon will probably fall mostly into being Dark-, Poison-, and Ghost-types (and btw, the Dark-type in Japan is actually called Evil-type).
Though of course the concept of yin & yang isn't just good & evil, but are actually meant to show that everything has an equal opposite (as well as both sides having a little bit of it's opposite in itself). The exact meaning of "Yin" is "shady place" or "north slope" while "Yang" means "sunny place" or "south slope". But of course after years the concept spread into meaning other various things such as:
"Yin" is usually characterized as slow, soft, insubstantial, diffuse, cold, wet, and tranquil. They are generally associated with Femininity, birth and generation, and with the Night.
"Yang" is characterized as fast, hard, solid, dry, focused, hot, and aggressive. They are associated with Masculinity and with the Daytime.
Honestly it sounds like if they were going to make something with Yin & Yang for these games, it'll probably be with the Legendary Mascots. And thus the Third Version will probably be Pokemon Gray and the mascot of that game will represent Qi.