Lady Squee said
Yeah, this.
I always interpreted the Pokemon canon as having real-world animals which the Pokemon lived alongside, at least in the earlier days of the franchise. Trouble was, real-world animals were hardly focused on, because, well... it only makes sense to focus on the Pokemon. There was really no good way to work them into the early games and, while some of the early cards featured real animals in the background, the anime never had much of a reason to focus on any real animals.
But then they started making more Pokemon species, and they realized that, even in the early episodes, real animals were hardly seen, so they sort of replaced more animals with Pokemon and sort of changed the canon so that all the animals were Pokemon, even if that wasn't originally the idea.
...Or at least, that's how I see it.
It's kind of like how the early games (and I think maybe a few episodes of the anime) implied that the Pokemon series takes place in the real world by referencing real-world places. But, again, only the early games ever featured such hints. For all we know, maybe that was the original idea (all the regions are based off of real-world places, after all), but then the Pokemon world expanded and took on more of its own identity so they cleaned up the canon and took out any ambiguity on that front. As much as I love the Pokemon franchise, I feel like their efforts at putting together an established canon were pretty sloppy in the early days. Seems like not even all the people working on the series were all on the same page on such matters.