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They never would have been brave enough because it would ruin the nostalgia bait but it would have been fantastic if they retconned Johto into the campaign. So, you had the new Johto Pokemon that were apparently native to Kanto and the new baby Pokemon scattered throughout the game to make the world most consistent. It'd also probably be too much content given how scarce the Sevii Island campaign really is overall, but it also would have been neat to have gone to Johto and it act as a prequel of sorts to Gen 2's story.
