Just created this for fun. My interpretation.
Pokemon are actually genetic experiments performed on regular animals based on things seen in Pokemon Go. This is why regular animals were seen/mentioned in the earlier games, they hadn't all been replaced yet.
>Zinnia says something stupid that can't be proved wrong or right
>Now everyone believes there is more than one universe
This is bullshit, there is only one universe and its lineal. Megas are rare, that's it