When I was a kid, I used to actually imagine my Pokémon acting in line with their natures and actually cared about each one having a different one since it meant my team would have "more personality" or whatever. That's what these are actually for, to make your team feel distinct and personal to you. And it makes sense considering how much bs is spewed about whatever bonds your supposed to share with your Pokémon, so attempting to make each individual one actually feel like an individual makes sense. Even if anecdotal, It helped me get immersed when I originally played through them. It didn't suddenly interfere with my fun then, and Idk why it should be the case now that I actually know what they do.
Obviously it was poorly implemented and has a lot of obvious flaws attached to it. Namely having to grind out for ideal comp mon for actual comp situations. But in the era of injecting, and hacking, still bitching about it now is just a clear cut case of nitpicky autism. Cry all you want about it still being bs or whatever, the fact of the matter it's an easily solved issue that is harped on by weirdly stunted manchildren who find themselves stuck in a loop of bitching about inconsequential horeshit thinking their spreading the light of truth cause gf is shit, as if this hasn't been obvious since, well, forever. If you really must participate in your crusade against the harrowing masses of corporate cocksuckers, at least spend time whinging about something of substance. Even if pretty much every single major flaw has been well documented and discussed to the point of pure redundancy.
tldr: Have sex.