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I've never read this fanfic before but it's breddy cool. I would be happy if they came out with a setting like this. I think your timeline idea would have been better suited for Celebi and Johto (though I suppose Johto was thematically more about the past and "Regina" thematically could be about the future.)
Fanartwise I can imagine a Kalos and Regina rivalry being a jokey kind of thing. That would be cute.