Rotoms and Shaymin too. I guess it could complicate linking theoretically, but I'm sure they could think of something. And I'm not saying they care that people are hacking the game, I'm saying that to me it's annoying that I have to wait years for them to get around to giving me my Genesect. Plus I don't know about other people but watching new pokemon slowly trickle out when new gen stuff is announced always gets me excited to play. Maybe releasing a small batch between gens would peak interest and keep people playing for longer.
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