Despite my love of the franchise, if only for nostalgic purposes at this point, I also love overthinking things. And Pokemon is just weird. For example:
1) It's Essentially Dog-Fighting
I know I'm not the first person to make this point, but it's still something that as a child, you don't notice.
You're still catching wild animals and forcing them to fight until they pass out for you. While technically Pokemon don't die (well...not during the gameplay battles anyway), they do "faint." I guess that's similar to boxing--punch the other guy until he falls down and can't get up again, but at least the boxer enters the sport by choice.
2) You Catch These Creatures
In the show, Ash often asks Pikachu if he wants to fight (the only Pokemon that he usually asks this, I'll note), and that's supposed to be the difference. Ash won't usually push his Pokemon to the brink. He cares about them. He asks if they want to fight, he stops the match before they can be badly injured, and he praises his Pokemon win or lose. But still, he is choosing to have them fight in the first place. Any injury they get is still his fault. It's not like they'd seek out other Pokemon to fight willy nilly in the wild--sure they might fight over food or shelter like any other animal, but it wouldn't be the same.
I know that we got our pets because we captured them and tamed them. But it seems weird that Pokemon are captured and forced into fights. There's a fan theory that Pokemon WANT to get captured and fight, that its in their genes, and the only reason they resist capture is to test trainers to see if that trainer is worthy of serving...but that test involves battling the wild Pokemon like a normal trainer battle until they're close to unconsciousness--and if you can poison them, put them to sleep, or otherwise weaken them, all the better--which hurts that whole "secretly wanting to get captured" thing.
And as seen in the video I linked above, Pikachu is clearly afraid of fighting Brock's Onyx because Onyx is huge and scary and could easily hurt Pikachu. Ash has to order Pikachu out there to fight--and Pikachu loses! Gets the shit beaten out of him. It goes so poorly that Ash consider forcing Pikachu to evolve to get the edge on Brock.
3) These are Children!
If you saw a 10 year old child approaching a skunk like they were going to try to capture it, would you stop them? Skunks are armed with the ability to spray an enemy with a concoction that would leave your child smelling pretty putrid, but they'd probably otherwise be fine. But what if that skunk didn't spray a stinky liquid, but instead blasted hundreds of volts of electricity at you. Would let them approach then? Probably not. And yet, that's the world of Pokemon.
In the first episode of the show, Ash is only 10 years old. Children that reach that age are allowed to skip school if they obtain a valid Pokemon Trainer's License, and instead go off into world to try to make a living as a Pokemon Trainer. These kids will now lack significant reading, mathematical, and scientific knowledge. And what are they doing to make money? In the game, you get money for winning trainer battles. So, the world economy is dependent on underground gambling over the fate of supernatural animal fights? School has been completely shirked in favor of this? How does anyone become educated if you can just skip out on boring old school and train and fight wild animals? There are scientists in this world, and doctors, and police officers...are they all failed trainers, or did they stay in school? Are there homeless shelters full of failed Pokemon trainers with no skills to offer the world?
4) This is the Entire World Economy
As I said above, the entire world is party to this hobby. It's not just one country's strange cultural sport--like American Football. This is the entire world. And here's the crazy part: it's not just a hobby.
Literally the entire world economy is based around these creatures. Literally every building or business that you go into is in some way involved in Pokemon.
- Pokecenter - These are hospitals entirely designed around the specific needs of Pokemon. And although they try to pull some mumbo jumbo about Pokemon all having the same basic DNA, that's still trying to figure out how best to heal an electrical mouse versus the ailments of a gigantic rock monster. And how the fuck do you heal a ghost?
- Pokemarts - These are the department stores of the Pokemon world. And yet, with the exception of the gigantic Pokemart you find in the big city, you can't buy things like water or food. Instead, you find potions (to heal Pokemon), pokeballs (to catch Pokemon), and other things specifically centered around the care of your Pokemon while you're out on the road. And even if we make the rational assumption that they do sell food and water and other normal supplies, it still doesn't change the fact that every single store in this world is the equivalent of a PetCo.
- Gyms - Places where you can take your Pokemon to train and battle the Gym Leaders so you can participate in the professional Pokemon fighting league. Every town has one.
- Even places that aren't necessarily Pokemon focused in concept are in execution: Safaris where you can go to observe and catch Pokemon, casinos where you can win Pokemon, museums dedicated to Pokemon history.
5) The Biology of Pokemon
Let's not forget the crazy scientific advancements these creatures imply. For one thing, not only has a species been discovered that has 151 different variations (going by the supposed fact that they all share the same DNA), but these many of the base versions of these creatures can transform with enough life experience into different variations of their original form. It's not just growing up, where the creatures change a little over time like humans, these are creatures that make gigantic biological leaps in an instant.
It's increasingly impressive when you consider some of the stranger aspects of Pokemon "evolution." For example, some Pokemon have relatively stable base forms and can only transform when being placed around certain elements. There are creatures that are ghosts--as in, they're dead and have come back as spiritual Pokemon. Some of them are animal-like, such as Pikachu, Pidgey, Spearow, but some of them are made from seemingly organic matter, like Geodude (a rock), Bulbasaur (a creature that's part plant), and Ditto, which is just an amorphous blob that just copies other creatures.
It gets even weirder when you realize that some Pokemon, like Clefairy, are supposed to have come from space. Or what about Porygon, a sapient crystal-creature that's supposed to have been created in a lab. Or Voltorb or Magnemite, which are just extraneous electrical/mechanical parts.
And yet all of these are supposed to have the same base DNA? Wat.
6) The Technological Advances
The technology in this world is astounding. First, let's look at the Pokeball, the standard way for capturing and keeping Pokemon.
Let's not overlook the Pokeball, though, a technological wonder. Basically, you have (supposedly) organic matter--Pokemon--being converted into pure energy and stored in a ball that can expand and contract at the push of a button. It can be as large as an apple in the grocery store, or seeingly as small as a large grape. Does this invention work on other creatures? Can normal animals be converted into energy and kept inside as well? Can humans? Or is it only coded to Pokemon DNA? Why wouldn't scientists invent a way to store food and other items this way. It would free up tons of space. If the Pokeball is destroyed while the Pokemon is inside, does the Pokemon return to its matter form, or is the energy just released?
Next, the Pokecenters mentioned previously? In the games at least, they can heal Pokemon in a matter of seconds. Does this technology work on humans as well, or, again, is it only coded to Pokemon DNA? what is it about Pokemon physiology that allows them to be healed so quickly.
Cloning is also a thing in this world. In the game, you receive a Pokemon fossil (A FOSSIL! AS IN, THESE THINGS ARE ANCIENT!!), and later in the game you clone it, revitalizing a once extinct species. And that's not the only instance of this: Mewtwo is also a cloned (and refined) version of an ancient Pokemon--Mew.
Telekinesis and psychic abilities are also confirmed. Abra can teleport, defying all sorts of physics.
Also: we know there's an afterlife. If ghost Pokemon are a thing, we know something happens (to at least Pokemon) after we die.
I could probably think of more, but this was as far as I got in my musings the other day, and this is plenty.
What separates this franchise from a very similar one like Digimon is that Digimon are, by their own admission, just data. These creatures are just sapient programming--impressive on its own right, but much more plausible than the world of Pokemon, where Physics just sits in the corner and sobs.