Ah, beta ideas. Let's look at them (and as always I'll give some of my thoughts on the subject):
1. The book firmly states that there "were" animals like dogs and cats existing in the world too, so don't get confused when they say that Squirtle is a turtle Pokemon. (Pokemon has always been a bit iffy about whether real world animals exist or not. It seems at the very least fish do as we always see people eating normal looking fish. Though that still doesn't answer the question like the names of real animals used as Pokemon's species names. I did hear one theory that, like how we use Latin words in scientific classification, real world animal names might not mean exactly the same thing as we know it ("turtle" to us is a animal (a noun), but "turtle" in the Pokemon world could just be a descriptive word (an adjective) for a Pokemon which is amphibious who's body is encased in a shell. Anyway, what I find kind of funny and disturbing is the "were" part. Is this hinting that originally Pokemon became sort of an invading species which killed off real animals and took their place? The next tibit enforces that idea even more)
2. It says that Pokemon suddenly appeared from nowhere and the species kept increasing. Nobody knows why and it's a total mystery. The direct quote from the book: "Why? How come? For what Pokemon exist in our world? Solving that mystery is equal with solving the mysteries of humankind." (Now obviously this idea has been tossed out due to fossil Pokemon. Though it does make you wonder what would happen to a society like ours if Pokemon were to become real, living things...)
3. The book says that "there is a legend that God created this world in a week. This God 'doodled' some extra animals in the seventh day. Those animals were born on a holiday, and they weren't ordered to 'be ruled by humans' or 'rule humans'. They are Pokemon." (So even in the Pokemon World humans don't listen to God (instead we catch him in a Pokeball). Also does this make Team Plasma's goal "holy work"? Though if originally god was to have created Pokemon because he was bored, what made Arceus create people? Were people an accident? A drastic evolutionary turn? For the lolz? As was said in a previous statement "Solving that mystery is equal with solving the mysteries of humankind."
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4. In the 18th century, zoology became a professional scientific discipline but there were some mysterious creatures that couldn't be sorted, like dragons or mermaids. Then Count Tajirin of France (... of course this is from Satoshi Tajiri, the creator of Pokemon...) discovered and studied Pokemon for the answer. (Wait, so there were dragons and MERMAIDS which weren't Pokemon? Also a lot of these ideas a bundled together so once one goes a whole batch of them do, including this one. Though I wonder what made Tajiri choose to have the first person to study Pokemon be a French (who has a Japanese name which is remarkably similar to his own...)?
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5. The book says that "this country is very similar to 20th century's Japan (Nippon), but there are differences." It's not clear that this 'Japan' means the real Japan in our world or Pokemon world's once-existed country, but I think it's the latter case, since every name or places are written in katakana. I guess it's a "similar-but-different-world" system like Rockman (Megaman) EXE's Nihon, Choina, Afrik, Sharo (from Russia), Ajia or Amerope. (Pretty much an idea which turned into the region system)
6. Nippon's capital is Tokyo, it seems. (... yes, Japan's capital in Tokyo, any reason why you included this geography lesson? (And for those of you who don't know, "Nippon" in Japan's Japanese name))
7. Pokemon are dangerous, of course. It is stated that not understanding fully about Pokemon and trying to train them is very dangerous and there are many people hurt or dead doing so. (This idea wasn't just thrown out the window, it was tied to a rocket and sent blasting through it! Yes, Pokemon are dangerous and hard to train, which is why kindergarteners are seen commanding powerful Pokemon...)
8. The Pokemon that enabled the invention of Pokeball is Okorizaru (Primeape). (That's interesting. Wonder why Primeape was chosen, maybe because it was the closest thing (at the time, this was Gen I) to a human a Pokemon has gotten?)
9. A gym leader is disqualified when s/he loses three times in a row. They often bribe challengers. Also it is a terrible job (cost a lot of money & the government support is not enough). (Now while the "losing their job thing after losing 3 times" (how did the Pokemon League expect trainers to get badges then?) and "Gym Leaders bribing trainers" (oh, that's how), the thing about being a Gym Leader being a terrible job might have been kept. Though it's not brought up front, in many medias like the manga the Gym Leaders often have an extra job or do extra things in order to make a living (infact this could have start showing in the games, how many of the Gyms in Unova serve a double purpose?))
10. This is why Takeshi's (Brock's) stepfathers kept running away. To keep the gym, Takeshi's mother got married again and again and had dozens of kids. Finally she ran away too, leaving Takeshi alone with his half siblings. (Wow... that's dark)
11. The reason why Takeshi (Brock) loves women might be this. He yearns for a kind, maternal woman who can take care of his siblings. (So Brock falling in love with every girl he sees isn't because he's horny, but rather because he was looking for a woman to help take care of his brothers and sisters. That's sorta sweet... in a still dark way...)
12. Kasumi (Misty) is 10 years old, same as Ash. (That or 11 which I've also heard, though eitherway Misty is around the same age as Ash which we all knew)
13. Kasumi's (Misty's) parents left too, leaving the gym to the girls. (Gee, with a culture that sensitive to losing you'd think that the government would re-think that whole "3 losses and your out" idea. Apparently it breaks families apart something bad)
14. Kasumi's (Misty's) sisters wear wigs for the show. They actually have black hair. (So is Misty also wearing a wig? It'd be kind of odd for her to be a red head while her sisters have black hair (not that that's impossible, just very odd and a bit unlikely))
15. When kids turn 10 they are legally treated as adults. They have to pay tax, get arrested when they commit a crime, can marry, can get a job, etc. (... I'm debating whether this is less or more creepy then the canon tale of People marrying Pokemon... However I guess this does explain why 10 year olds can just go off on a journey without parental supervision)
16. When they turn 10 they can choose to keep going to school or go on a journey. (Hmm, so I wonder if the "Gen I was actually suppose to take place over Summer Vacation" is just a rumor or became the "alternate" idea when the "your an adult when your 10" idea was thrown out?)
17. Most of the males in the world try to be a Pokemon trainer, and of course, most of them utterly fail hard. Then they just become incompetent adults. (And that's how we got politicians *rim shot*)
18. That's why most of the workers are female. (I'm guessing this is referring to the Nurse Joys and Officer Jennys? Then again the Pokemon would does seem neutral when it comes to gender and jobs, though I always thought that was more because Pokemon took the brunt of the hard work. Though if this is talking about the Nurse Joys and Officer Jennys, then how does it explain why they all look alike? Or were the nurses and officers not suppose to look alike and it was changed to how it is now?)
19. That's why Satoshi's (Ash's) grandfather and father is missing. They went to Pokemon journey and disappeared, achieving nothing. (Once again, pretty dark. Maybe the government should re-think this whole "Pokemon trainer" thing and make it a harder field to jump into... oh wait, that's right, most of the politicians are incompetent males because they tried and failed to go on a journey)
20. Satoshi's (Ash's) mom married when she was 18. She (then with Satoshi's grandmother) ran a small inn/restaurant, and Ash's father was a Pokemon trainer rookie who stayed at the inn. They fell in love so fast and got married so fast. Then he left so fast. (I wonder if Ash's father even know he has a son... once again, a dark thought. However I do think Delia owning a restaurant which she inherited from her mother is a canon)
21. Shigeru's (Gary's) father (Prof. Oak's son) is the mayor of the town. Shigeru's 'girlfriends' are the girls his father employs for election campaign. (Interesting. I know in one of the mangas it's actually revealed Gary's parents died in a car crash and always assumed that as a canon for most of the other medias. Now I wonder what is the deal with Gary (or Blue in some of the continuities) parents)
22. According to the book, a talking Nyarth (Meowth) 'cannot exist and must not exist'. (... is that hinting that a possible side plot was going to be about killing Meowth?...)
23. When Nyarth (Meowth) translates what Pikachu is saying, Musashi (Jessie) and Kojiro (James) are surprised that he can understand it. Then Nyarth says "I practiced hard to be able to do that". This implies that different Pokemon species have different languages and they normally can't understand each other. (While this would actually make sense real life wise, obviously it was made that, despite each Pokemon only being able to say it's species name, every Pokemon "talks" one language. Though I wouldn't be surprised if each species has a set of words only their species has a meaning for. But wait, how did Meowth learn the other Pokemon language then? He spent all his time just learning how to speak human. Also does this mean Meowth somehow learned over 100 different languages?)
24. Musashi (Jessie) and Kojiro (James) actually used the names of Miyamoto and Sasaki when staying in a hotel for recuperation (disguising themselves as a couple and Nyarth (Meowth) as their kid, putting bandage around his whole body). The hotel owner thinks that it's weird that they are married but have different surnames. The book doesn't say about if they are their real surnames or not. (So in other words even when they were trying to stay low the Rocket Trio were incompetent by not choosing the same surname despite acting like a married couple with a child)
25. Musashi (Jessie) and Kojiro (James) hold a record in Team Rocket for eating one-year-old, moldy fried rice and being okay. (They would...)
The other post is about a task Jessie did for Team Rocket so I'm not going to post it. But eitherway, very interesting. Seems like Pokemon was going to be a much darker world then we know it as today... though then again, exactly how much of these ideas have been thrown away? And was there and could there still be other hidden "darknesses" that we don't know about? Well I guess we'll either never know... or will find out soon. MUAWAWAWAWAWA!