Gen I and II are part of a drastically alternate universe. Rather than having more minor differences, such as details or chain of events, the universe itself is very different; Pokemon's diversity didn't go past Celebi, and their biological structure functioned in an alternate way (this is why...
Fairy type was a very recent discovery. A few months before the events of XY, the 3000-year-old energy from the Weapon caused mutations in many different Pokemon in Kalos, changing their typing to Fairy and giving them various resistances, weaknesses, and powers that hadn't existed before. Pure...
N can understand Pokemon because he's from the Mystery Dungeon world. In the Rescue Team series, it's shown that travel between the human world and the world of Pokemon is possible, and the Explorers series implied that humans existed in that world, and could apparently communicate with Pokemon...
My friend and I came up with the real-life equivalents of the evil teams:
Team Rocket- the Mafia
Team Magma/Aqua- two feuding rival gangs
Team Galactic- Crazed scientologists. We couldn't think of a better one... but hey, they're all about science and the universe, so yeah...
Team Plasma- A...
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