>>35401341back in the sprite era it was made as literal palette swaps and couldnt be too drastically different as it wouldn't look proper in the style or s/t. im not sure exactly what the explanation was but sprite shinies are literally just palette swaps so that plays a factor into the design. And for gen 6/7 james turner confirmed on twitter that the people who design the pokemon design the shinies now (they usually didnt before)
using this information id say we can assume gen 1-5 shinies were picked just to look good on the sprite itself. for example some pokemon use the same color for 2 different color parts of their body. i cant remember a specific example off the top of my head but lets say a pokemon is yellow and brown, it could use the same brownish color for the yellow outline as well as the brown shading, but if you wanted to replace the yellow with red and the brown with blue, it wouldnt work on that sprite because the reds outline and the blues shading shouldnt be the same color. does that makes sense? its hard to explain and im very tired. but in gen 6/7 they can avoid this with 3d models because its not just a limited palette swap anymore, and some gen 6/7 shinies might be more different than gen 1-5 shinies because the people who design them are picking the shinies now.