And yet it's true. Did you honestly expect that Game Freak had people painstakingly swapping the palettes of every Pokemon? That's too time consuming and expensive to dedicate their resources on. Look at shiny sprites again.
I'm sorry but
what? Do you have any experience doing this sort of thing or are you just talking out of your ass? Because I can guarantee that if you know what you're doing, making a shiny version of a texture for a model takes less than a minute to make.
Let's suppose they have every different color of a model on a different layer in a .psd file. If you look at existing textures, you can see that they have very basic shading, so those are probably on a separate layer as well. Now all you have to do is move around the hue slider a bit for each layer until you get your resulting shiny texture.
Virtually any Pokemon with the same base color has the same palette swap, as the games developed better graphics and more colors, palettes diversified so in earlier generations you see a lot more of it. Even still, Ferrothorn's spikes and Trevenant's leaves have the exact same green and both turned the same red in the shiny versions. There are a few exceptions where Game Freak wanted specific palettes or specific colors on the palette to remain the same, but those remain rare.
Pokemon with similar colors having similar shiny colors is an artifact of the old games and their sprite-based images. Since they all used palettes, shinies were made by just making the sprite use a different palette, which is why so many old pokemon have a bright pink or green shiny. Once they moved to standalone textures like in XY, they were able to color shinies however they wanted, which is why there's so few shinies (if any) that are either bright pink, green, or look almost identical to their base colors (like gengar and garchomp).
Rain, sun, hail, sand, delta stream winds and primal weathers?
I wonder what these are for.
bug, rock
flying, grass
dark, steel
water, electric
ground, fighting
dragon?, fairy?
fire, psychic
poison, ice
ghost, normal