Things that don't make sense in Pokémon

Hi, it's just a nobody here in the community and I wanted to ask a couple questions for a fanfiction I want to write about Pokémon.

All small things aside, like Pokémon being a typing they should be, Pokémon being a typing they shouldn't be, what are the main concerns in the world of Pokémon? More specifically, what are some big topics that actually don't make sense in the Pokémon world?

I've been trying to find big topics that don't seem to be logical or at least be consistent with itself and I want to know what topics don't seem logical to you guys. Hell, even the whole notion of Pokémon actually existing at all is already baffling enough, but whatever. Please feel free to ask your own questions and pose your own answer to it. I myself have some questions in my head and I would like answers.

1) How does evolution work? In the real world, according to the theory of evolution, species that were unfit for their environment died out, while those who had successful adaptations went on to live and make that adaptation more pronounced. In that case, why are there multiple Pokémon species running around? For example, a Charmander is clearly weaker than a Charizard and, since they're two different species, shouldn't the Charmander have died out? Or is like puberty and growth in where a base Pokémon like Charmander grows into a Charizard? I don't know. I find the whole notion of light covering a Pokémon then it's suddenly evolving. (Also how can Pokémon like Pikachu evolve in the wild naturally; shouldn't they need a Thunderstone to evolve? How could there be wild Raichu? Answers please lol)

2)How do TMs work? Are TMs machines that one applies to the Pokémon via their Pokéballs? I wouldn't be surprised since Pokéballs seems to be advanced technology. I, for one, have no answer to this question and can't even think of one that would make the most sense. The closest I've gotten involves genetic code being turned into binary by the internal technology of the Pokéball and somehow using a TM that has code in order to overwrite Pokémon memories or something, I don't know.

Thanks for giving your own questions, I really appreciate the help.

-Shadierre

yeah evolution is definitely pretty nonsensical given how it works in real life. a better term for "evolution" in the context of the Pokémon world would be metamorphosis or something like that. in real evolution there's no sense in which an individual animal can "evolve" - evolution is something that happens to a species as a whole, and over millions of years at that.

How the hell it's still going after 21 years

I think Pokeballs are the biggest one, for me. I know some effort has been made to explain what is inside them, but I still don't understand how a Pokemon can be materialised and de-materialised at will when it's captured inside a Pokeball. Something like Porygon I can understand, since you could just compress the data, but most Pokemon are organic beings, so how do they not just...turn into goo, when someone shrinks them. Like that one guy in Ant-Man.

For that matter...some Pokemon themselves don't make sense. Like...Cubone. It wears the skull of its dead mother, so do all Marowak die the second they give birth? But if they lay eggs - and why do all Pokemon lay eggs?! - then...who takes care of them between the time they're laid and the time they hatch? Alakazam is another one. If it has an IQ of over 5000, why is the world not run by Alakazam? Why does it allow itself to be confined inside a tiny ball and commanded by an ignorant 10 year old?

Also, how the hell are high-tech gadgets made from fruit that grows on trees? Apricorn Pokeballs are just...what. Why do they need to made from Apricorns? What properties do they have that makes them special?

Shouldn't the world just turn into the second Pokemon movie when everything goes to hell whenever someone captures a Legendary Pokemon? From the third game onwards, Legendaries have been presented as pretty damn crucial to the region's functioning, and some of them are even deities. Logically, every time someone catches a Legendary all hell should break loose...and the offender would have pretty much everyone in the region after their blood. How beings of phenomenal cosmic power can be confined in such an itty-bitty living space defies comprehension too.

I'd love to know how society works in Pokemon, too. There are just...so many holes here.