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I think the biggest fix would be just removing IVs. They don't add anything meaningful to the game or any strategy to Pokemon battles, unless you're running a meme Trick Room team or something. Natures, abilities, and EVs already allow the player lots of freedom in how they want to build their Pokemon. IVs don't do anything other than make 99% of Pokemon useless. I don't think removing natures and abilities would really help. Some Pokemon have different builds that use these different aspects, and even if one might be more optimal than the other, it allows the player to play around and build different teams that someone might not expect. There's good arguments to be made that these things should be kept. IVs, however, are shit.
GameFreak seems to know this, too. Every new game they introduce more and more items to circumvent the absolute shit grind it used to be to breed good Pokemon, but at this point they may as well just change how Pokemon work and save everyone the time.