Why not DLC-style Pokemon. A sort of buffer of new pokemon between generations. I think it would be a lot more exciting to learn about Kaldeo, Meloetta, and Genosect months or years after B/W was out and to learn that they would be downloadable. It would be a lot better than "hey guys these pokemon exist, and you can't have them, oh but here's an event Mewtwo that can chill with the other three in your boxes"
They sort of do. FireRed, LeafGreen and Emerald introduced different Deoxys formes and Platinum had a new Giratina Forme. Completely new species might complicate link battles. Also they might not care that people can fish through the game's data for unreleased Pokemon.
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Pokemon VGC2011 NW Regional - Top 8 Pokemon VGC2011 US Nationals - 54th place
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.