Pokemon were never meant to just be animals tho. If you look back and read all the Gen 1 material and the script to Red/Blue, it's pretty clear the original vision of them by the developers was that they were like cryptids and youkai. That's why the Pokedex gives them classifications like "Mouse Pokemon", because those normal animals were meant to exist in the Pokemon world and the Pokemon were just like mutated or supernatural versions of those animals. Considering cryptids can include aliens and other weird shit, and youaki include inanimate objects coming to life, having a few weirdos like Voltorb, Magnemite, and Grimer fit right in.
There's some remnants of this in the early anime, where very occasionally a regular animal would pop up on screen.
Game Freak didn't start treating Pokemon as the exact equivalent to animals - to the point real animals don't exist in the Pokemon world - until around late Gen 2 ~ early Gen 3, which is also the point where series creator Tajiri stepped down and was replaced my Masuda, and Pokemon started slowly losing its SOVL. Even as a kid, it was really obvious to me how "gentrified" Pokemon became in Gen 3. All the world-building was fully hashed out for the sake of maximum marketability, any edge that you could argue existed previously was filed off, and the games fully fell into their comfortable pattern of rehashing the game structure of collecting 8 badges across a region, sometimes fighting an evil team with the climax between badges 7 and 8, fight your rival one last time in Victory Road, and then fight the Elite Four + Champion. Gen 3 and 4 lacked any sort of experimentation that signified Game Freak might have some ambition or be going anywhere, like how Gen 2 gave you two regions to explore.
I guess they did pioneer having the box legendary be a part of the plot, but that's not exactly a good thing when it also corresponds to them introducing version-exclusive legendaries, something the first two gens never did. In Gen 2 the version you played decided which between Ho-oh or Lugia you could obtain faster (just before the Elite Four), but you could still catch the other in the post-game. Now you need to find someone willing to trade away their one-of-a-kind catch or just buy both versions yourself if you want to catch 'em all.
Not to say I hate the Gen 3 games. Natures and Abilities were a good idea, FRLG is mostly an improvement over Gen 1 in many ways, and Emerald is alright being a definitive version that rebalanced the boss fights to not be total pushovers and added the Battle Frontier. But I can't help but find the original Ruby/Sapphire versions to be kind of soulless and emblematic of the series' eventual decline. The base gameplay being improved from Gen 2 to 3 doesn't matter much if the game using that gameplay is still just an uninspired rehash of RGBY with braindead easy opponents to fight in the story mode. And the same is true of Diamond/Pearl, which is the exact same structurely as RS, but with added jank because Game Freak couldn't into programming for the DS. It was saved massively by the B-team completely redoing so much of it for Platinum.
