>>21994079>rabbit holeLeAp PeSt DoOr
It's not that hard, really. Third versions are generally canon to future time periods, as showed by G/S/C and HG/SS Red having Pikachu as his primary Pokémon and all three Kanto starters in his party, and by Cynthia's reference in B/W: "You certainly bear a resemblance to that Trainer who faced Giratina..." Clearly implying it for Yellow (and never-made Universe B Yellow remake) and Platinum at least, and thus probably also true for Crystal (and never-made Universe B Crystal remake) and Emerald. Black continues into Black 2, White continues into White 2, every game is an alternate timeline of its universe and every single playthrough is an alternate possibility for that timeline (akin to the multiple time loops in BlazBlue: Calamity Trigger, but not as explicit, nor as dark, and it's unlikely that anyone except certain Legendaries are capable of remembering other possibilities and it doesn't affect them as much). Data can be transferred between alternate timelines, even among time periods sometimes (like between R/B/Y and G/S/C, or between B/W and B2/W2), and that includes Pokémon and items converted to data.
There is a question for what counts as canon between OR/AS and X/Y, as the Universe A and Universe B formulas aren't as clear to work in Universe C yet, but if there are any further remakes or third versions that'll become clear. At the very least, there was a comment about Blue (Green in Japan, Gary to anime fans) in Y that implied that some version of the Generation 1 story happened.
