Early in the episodes, you see real life animals..*cackles*, You see fish in Misty’s aquarium, you also see fish in the bottom of the ocean when S.S. Anne sank, You could also hear bird calls in the distance and there was a worm being eaten by a pidgeotto, and then there are all the pokedex references. I’ve heard stuff like “oh they didnt have enough pokemon back then”, and “the pokedex are like that just so you can relate, but wouldnt it be cool if we could claim that the animals were secretly

This question has fallen afoul of Tumblr’s arbitrary 400-odd character limit, and was supposed to end:
“…going extinct, and noone gave a crap about it cuz pokemons obviously the "superior species”, what if a field inhabited by wild boufalants was once a home for regular buffalos or something like that. idk, i get curious about these things cuz the creators are so vague in these areas"

Anyhow, I shall answer thus:
Well, yeah, the out-of-universe reason is probably more or less as you suggest.  Bear in mind that, when Red and Green were released, no-one at Game Freak had any expectation that there would ever be more than 200-250 Pokémon if that, and they certainly didn’t anticipate that Pokémon would become the global phenomenon it has.  I think that, in the early stages of the franchise’s development, they probably did assume that there were a bunch of regular animals filling all the ecological niches that Pokémon didn’t… fish, birds, insects, in the second episode Ash even mentions cows.  It’s only in the last generation or two, I suspect, that they’ve consciously begun to think they can build an entire ecosystem out of Pokémon alone.

This is all very well for the designers, but we the fans now need an in-universe explanation for the disappearance of those animals.

Your interpretation is… rather dark, and also confronts us with the question of why the real-world animals haven’t already gone extinct long ago.  Pokémon are basically animals that can defy physics in one or more ways, so there really shouldn’t be any contest there, regardless of human activity.  I think it sort of implies, actually, that Pokémon are relatively recent additions to the ecosystem and are replacing the other animals one by one as their foothold grows, which might be a fun basis for a total reinterpretation of the setting, but can’t really explain the version of the world we have.

I guess if I had to explain it, I’d tell you that the real-world animals are there, all right, we just don’t care about them because they only fill the less eye-catching ecological niches (in short, there are no buffalo or giraffes, but there might be mice and snails).  Whenever a particular area lacks the Pokémon necessary for filling a particular niche, there’s a real-world animal there to take its place, but no-one wants to hear about those.  I have no explanation for the cows, because it stands to reason that farmers would import and export Miltank all over the world while regular cows would be herded only by a few die-hard traditionalists in the regions they originally came from.

I think for me the big question is whether Pokémon are a monophyletic group or not – that is, whether they share a single common ancestor with no descendants outside the group.  The whole issue would actually become a lot simpler if we assume Pokémon are paraphyletic, like fish (that is, dog Pokémon are more closely related to dogs than they are to other Pokémon, and so on) but that seems to be at odds with the way scientists in the Pokémon world talk about them.  So, yeah, I don’t know.