My theory is that some pokemon learned how to mimic what their names sound like after centuries of humans calling them those specific names, and some names were created based on what specific sound the pokemon makes.
A lot of pokemon don't say anything. They roar, growl, or something else. I think that some are named after what they say and are named something similar if they evolve into something that doesn't say anything. Like Charmander, Charmeleon then they name Charizard to keep it relevant. I may have a bad memory but I don't think weedles, kakunas and beedrills say anything, so their names are based from the life stages of a bee. Same with caterpie, metapods and butterfrees. Like I said though, I have been out of the pokemon loop since the original season ended so, my memory may be a little cloudy.
The ones that actually say something are probably named after what they say since otherwise they would have had to learn how to speak through the name that was given to them.
Pokemon saying their name is a feature almost exclusive to the show. It wasn't something the creator of pokemon wanted in the game which is why you get the shrill screeches (what they really sound like) in games.
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