This is already a theory made by many Pokemon fans. However I have my own theories that are part of the fan theory.
Okay, if any of you noticed that if you watched the anime of Pokemon and played the games you noticed that your trainer you play as in game and that Ash and Dawn and maybe Misty if I can remember correctly from my childhood never really known about their father in their life.
Your rival in LeafGreen, FireRed (and originals Green and Red) Gary Oak (or whatever his name you chosen him have) has no parents whatsoever. He is pretty much a orphan who was raised by his grandfather Professor Oak.
You noticed that there is a lack of a major adult population in the Pokemon world in the games. It usually a gap between younger and older generations. And you've noticed that their aren't a lot of people for a high population in a region in the games unlike the anime.
And when you face the gym leader Surge in LeafGreen or FireRed he brags about how some electric-type pokemon saved his life during the war.
This fan theory pretty much states that before the story of games of either LeafGreen or FireRed (or original Green or Red games) there must of been a violent and bloody massive war called Great Pokemon War where many people died along with pokemon by using them in war to fight as well as using man-made weapons such as tanks, fighter planes, guns, etc...
This explains the reason you never knew your father in the games, because he died in the war. Gary Oak's parents died in the war which Prof. Oak had to raise Gary by himself. The reason not many adults who are in age of 30 or 40 or 50 exist because that they've all were killed in the war.
Orre from Pokemon Colosseum and Pokémon XD: Gale of Darkness the region is mostly a desert, pokemon are rarely to be found and can be found and caught in certain places of the region of Orre. There are no gyms, it has a huge crime rate. I did my research on the region and it comes to my conclusion that Orre was a region with more habitable places perhaps more urban had forests. But during the Great Pokemon War the region of Orre was hit by nuclear attacks either from Hoenn, Kanto, Johto or Sinnoh or perhaps all three of them nuked Orre to the point that it became a desert by radiation, forests were what is now desert, pokemon that once lived throughout Orre either became endangered or extincted from the nuclear attack as well as the residents of Orre themselves became so sparsely populated. This explains why that their aren't many pokemon in Orre, why their isn't many people and why it mostly covered in a desert and has a huge crime rate.
But I also researched other things as well on Bulbapedia. I took notice that since the Pokemon Rangers also exist then how did they came into being exactly then?
My theory is that during the Great Pokemon War, that perhaps the Pokemon rangers became major in native regions of Sinnoh, Kanto, Johto, and Hoenn. However the governments of the regions did not agree to the way how Pokemon Rangers caught pokemon and how they tamed them, which I believe led to dispute and then bloody conflict between their native regions.
This perhaps in my conclusion made regions like Almia, Forie, and Oblivia become populated by rangers who fought bloody war for independence from Sinnoh, Johto-Kanto, and Hoenn.
Thus Almia split and became it own Pokemon Ranger region from Sinnoh in a war of independence. Same with Oblivia and Forie from Hoenn, possibly Forie could of been a former colony to Hoenn and became a independent region in a war against Hoenn which the rangers there won.
As a result the Great Pokemon War was basically a world war which was fought between both Pokemon and also man-made developed weapons like guns, tanks, fighter planes, battleships, and of course nuclear weapons eventually as well.
I believe that there were surely more than one Great Pokemon War, there could of been their World War I and World War II, which could explain that the current Great Pokemon War could of been a deadly World War III in the Pokemon world.
First Pokemon War is to our reality of World War I, Second Pokemon War is to what World War II is in our reality, and for the recent one that happened before the story of games of FireRed or LeafGreen is the Third Pokemon War, which is to us similar to our hypothetical World War III, we hope that will never happen ever.
Thus this probably explains to us why when you begin your journey in the Pokemon games why you have no knowledge of who your father was, why there is a lack of adults throughout the world in Pokemon. There are rarely few adults that are in there 50's, 40's, 30's, or late 20's. But those who are around probably are lucky veterans of the previous Great Pokemon War, thus they've became gym leaders or Elite Four members.
However that does not include that every Elite Four member or gym leader of any region is a veteran of the previous war. Some for example like in Sinnoh the rock-type gym leader, Roark is the son of the steel-type gym leader, Byron in Sinnoh. Thus the steel type gym is a former war veteran while his son was not, since he was not born during the war. Not to mention we hear no mention of Roark's mother, thus I believe she was also a veteran in the war, she survived gave birth to Roark, but later killed herself due to major PTSD. Brock and Misty the gym leaders in Kanto are not veterans due to their young age. However since Brock in the anime has a family it is possible that his mom or dad were veterans of the Third Pokemon War. Whitney from Johto is not a veteran since she was born after the war. Sinnoh's gym leader Gardinia is perhaps a veteran along with Crasher Wake, Volkner (he wears a military uniform of which that Ottoman troops wore in World War I, perhaps passed down from a ancestor from the First Pokemon War), and Fantina are veterans while Candice and other young gym leaders of other regions are not veterans due to appearing to be born after the Third Pokemon War.
Gyms and Elite Four leagues of any region are what I think in my theory is what helped rebuilt the societies of regions after the the Third Pokemon War. This means they have never been in existence forever in Pokemon's history of their world. Before there probably was no such thing as the Elite Four, Battle Frontier, or Gyms because they did not exist since it was because people the Pokemon Wars were fighting for war and not for sport or should I say even entertainment either until the end of the Third Pokemon War is when people made them and began to stop using Pokemon to kill one another in war.
But what about the region of Orre I mentioned earlier? How come it lacks regional gyms and a Elite Four.
Simple due to being hit hard in the Third Pokemon War, they did not recover since and thus perhaps only were able to fight for sports in their own system instead. And plus the region being in what I said earlier was hit by a nuclear attack from other regions such as Johto, Kanto, Sinnoh, or Hoenn must of lead the region of Orre never to have gyms or their own Elite Four because simply the region is pretty much has no form of government. Thus Orre is a region that is in anarchy since the Third Pokemon War.
We notice that the main character in each of the games in that series wakes as a Pokemon and remembers that they were human in the past but barely can remember what had happened to them.
My theory suggests that the universe of Pokemon Mystery Dungeon is a alternated world of Pokemon where perhaps that the Third Pokemon War ended in humanity become extincted from a horrible nuclear global war with each other and that Pokemon managed to survive and became intelligent to make their own homes and perhaps speak language like that formerly humans had spoken before they died out. ====
So your main character in any of those games is one of the few or if not maybe last humans in the alternate world who managed to survive the Third Pokemon War which led to human extinction. How he/she became a Pokemon is still questionable and debatable. However I can explain this.
Remember when in Pokemon LeafGreen or FireRed that you travel to Cerulean Cape which is a dead end and there is a located a special Pokemon house which is also a lab. Bill who had a machine that was able to change himself into a Pokemon either by curiosity or perhaps a accidental discovery.
Which explains how he is able to speak to your main character (who is the trainer) and tells you how to operate the machine in order to turn him back to a human.
This is perhaps what explains how your main character in Pokemon Mystery Dungeon had been formerly a human being only wake up and remember nothing how they've became a Pokemon. Due to the Third Pokemon War is a huge blank in memory of what happened before.
Pokemon Trading Cards universe (which had a game too) where it is located in a place which is a region called Holon. Where is Holon exactly? Where is in the Pokemon world? Is it Kanto? Johto? Unova? Kalos? Sinnoh? Hoenn?
I think it actually all of the regions including Orre and the Pokemon Ranger regions too.
Holon in my theory of the Pokemon Trading Cards universe is another alternate universe of the Pokemon world, the exact opposite of Pokemon: Mystery Dungeon series.
Third Pokemon War happened like in the other universes but instead of humans being ones to be become extinct it was Pokemon instead. People in Holon Universe always wondered why they aren't any Pokemon in their world anymore. Reason to that is because during the Third Pokemon War it got so bloody and messed up that Pokemon began to die out from being used to fight in the war. Not to mention nuclear weapons killed perhaps millions of wild pokemon as well.
Why do people in Holon Universe (Trading Cards) use cards instead of Pokeballs? They couldn't use Pokeballs anymore since when Pokemon became extincted they had to stop using them.
That didn't make people stop fighting for entertainment and sports. Thus they mass produced Pokemon cards and started competing against each other instead of using real pokemon. They did it so they could remember Pokemon so they wouldn't of been forgotten forever.
If there is any pokemon that are left in the Holon Universe, they are either fossilized pokemon (which due to the lack of technology from the dreadful Third Pokemon War made technology kicked back a bit thus people aren't able to bring fossilized pokemon back to life) or are legendary pokemons perhaps Mew survived and it hiding in the world in the Holon Universe as said with some perhaps surviving legendary pokemon elsewhere in the world. The reason they don't show themselves present to humans is because they are still afraid of them ever since the Third Pokemon War.
As I finally wrap this up, this is my expanded theory that is relating to the fan made Pokemon theory of the Great Pokemon War. I hope anyone of you my watchers might agree with what I said.