These are some theories and ideas I thought of concerning various aspects of the Pokemon World. They are all ideas I had thought of over time and have been developing them. I haven't been involved much in the Pokemon fandom much for a while nor have I played or watched any games/anime for a long time but the memories and thoughts are still there.
Anyway, I will start with the Mystery Dungeon series as that is my favourite series and depicts the pokemon in the most human-like and anthro-like possible. My belief is that these games are probably in the same world as the main series games but set in an undiscovered part of the world, probably an island or a continent in the far south of the planet. Arceus, who is the lord and protector of the planet takes great watch at this part of the world as it is the last safe haven for any pokemon here who have developed into a fully developed civilization with towns and cities. Like with humans, you get good pokemon and bad pokemon. Most of the human world could have become like this but is instead dominated by human-made towns and cities and trainers who have captured many pokemon destroying families and ways of lives. Some pokemon who have witnessed such activities hate humans and do their best to keep them away. Those living in the Mystery Dungeon parts are aware of humans although some don't believe they exist. Some humans, usually trainers get sent to Mystery Dungeon while being turned into a pokemon as punishment for certain actions, which is usually caused by Arceus. In the Mystery Dungeon games, the pokemon are able to talk but in actual fact, this is the case everywhere. All pokemon can talk.
It is only humans who cannot understand them and is a curse placed on humans in the early days by Arceus as many betrayed the trust of pokemon and tried to destroy or capture them so Arceus took away a lot of the abilities humans once had such as being able to understand pokemon. Seeing a lot of how humans act now such as with the various Teams (Team Rocket, etc), Arceus believes that most humans are scum and his biggest mistake. Arceus created humans as guardians to care and protect the pokemon later after all the various species had been finalised but a chain of events caused many to go corrupt. This angered Arceus so he cursed humans, erased all the memories of the humans living at the time around the world and had it so humans and pokemon were seperated further. A brief war between humans and pokemon occurred causing unrest afterwards, which has never fully recovered even though there are good humans about what have existed since that incident. Many pokemon, however, still do not trust humans and do whatever they can to deter them.
Arceus has plans for the pokemon world and has been observing humans closely. Recently, there has been a new breed of humans known as The Emeralds, similar to Earth's Indigo/Crystal Children. These are similar to what humans were originally like in the Pokemon World before Arceus's wrath. N is one of these type of Emeralds. Although there are others. Emerald people can understand pokemon and are more in tune with the surroundings. Arceus has done this in order to slowly start a new age of humans and pokemon. He wants evil humans such as those in Team Rocket, etc destroyed and will allow the pokemon themselves to capture and execute members. Asa pokemon himself, Arceus always prefers pokemon over humans and even regrets ever creating them sometimes.