>>40046805I think it has less to do with the actual transition and more to do the fact that a lot of the sprites didn't give the Pokemon the proper amount of bulk for their bodies to make sense. Having massive limbs and a tiny little torso and abdomen just makes them look like noodle monsters. This isn't really a problem with the sprites since you're only seeing them from certain angles and in very specific poses. In 3D you need to be able to see them from every angle and they actually need to move around with a certain degree of anatomical accuracy. In terms of giving them all more realistic proportions you could either shrink their limbs to fit their bodies or expand their bodies to fit their limbs, and they decided the latter was the better option. This doesn't explain all of them, there are some like Blastoise who is just way too fucking fat now, but it explains others that look a little off like Lugia and Haxorus.
There are also a bunch that are in dire need of better idle stances. All of the gliders, Marshtomp, etc.