i have taken a look at the Pokemon Ranger, Mystery Dungeon, and the Orre spinoff games and came up with this theory that they're somehow related too the main series games i will talk about their relations in order
Pokemon Ranger: it takes place a few decades before the main series. there have been no PokeBalls seen or used in the series at all. Drayden in Black and White mentioned how there were no Pokeballs when he was younger... given this similarity i drew myself to this conclusion (feel free to correct me if get anything wrong) also the technology used in the Ranger series doesn't seem as advanced as the technology used in the Main series
Pokemon Mystery Dungeon: alternate timeline, N wins climatic battle in Pokemon BW. i know many people may have touched upon this before but i'll still write this post as is. Humans have been mentioned and acknowledged by the Pokemon in these games, this shows that at one point the Pokemon in this series have made contact with Pokemon in the distant past, perhaps some of the ruins in that series were man-made. also worth noting, the Pokeball design has been referenced by the rescue team/exploration team, etc. badges, also TM's! they exist in those games too.
Pokemon the Orre saga (no official name is given to this series): either alternate timeline where Lysandre wins and uses the ultimate weapon or the events of X and Y played out exactly as they did where you won. for the former option: some team flare members may have possibly kept some of their Pokemon to survive in the new world, the aftermath of the ultimate weapon has desertified most regions. as for the latter option, it could be possible Lysandre was right about the worlds dwindling resources and humanity's continuing course of actions are why the regions are like the way they are.