For me it´s still the fact that Charizard is a Fire/Flying type (and not a dragon), while it is a… Dragon. To stay with Charizard, another fact that got me a bit confused back in the day whas that in Red/Blue it could not learn Fly.
I also kind of love the fact that Gengar (a flying ghost) get´s KO´d by earthquakes.
Ghosts can choose to either maintain some badass ethereal form or possess literally any object they want to. Given this choice, a substantial number of them choose to possess things like…teacups, tree stumps, and sandcastles.
Given humans’ general proclivity toward anger, Hatterene canonically tracking down and beating the hell out of anyone with a negative emotion nearby is simultaneously hilarious and terrifying.
Also Volo has togekiss as his ace, and several of togekiss’s dex entires note it won’t appear anywhere where there’s conflict. Togepi also evolves via happiness. So you can canonically be a psychopath religious fanatic, and still treat people right
In fire red exclusively, Indian Elephants became a metric by which you could measure a Pokemon’s strength. Indian Elephants were mentioned in gastly and raichu’s Pokedex entries
They drink a lot of water and eat a lot of Wishiwashi to gain enough weight to swim/dive and prevent floating. At least, that’s what the Pokearth documentary claims, not my words.