>>57101342In the case of the starters, I bet it's because "they don't want players to feel bad that their 'First Partner' can be outshined visually by a rarer variation". And since the starter picks specifically are shinylocked, thus meaning you have to breed to get shinies of them, that can extend to "Nor do we want to dull the experience of getting your First Partner Pokemon by a slim promise of getting a variation that's visually different from all the others."
In the case of Pokemon in general, it's to make it so you have to spend more time identifying those shinies due to how assfuckingly easy it is to boost shiny odds. Shiny Charm, Sandwich Boosts, Outbreak Chains, so on, they make it so you'll outright fucking drown in shinies. But if the shiny you're looking for is barely different from the regulars, that means you have to slow down and waste more time discerning the differences rather than seeing a splotch of, say, blue amidst a bunch of greens.