For the times the meshes are nearly identical (Swampert here) both have the same poly count and pose as both use the same sculpt, but the bone hierarchies are different, with XY (right) having a lot more extraneous bone end tips for IK anim assisting, while Pokedex 3D Pro focuses on extra bones being setup for the camera origin. Textures oddly have completely different UVs
We even have some Maya sculpt files in the leak for XY meshes before they retopo'd as lower poly models
Skinning even differs for mons with the same mesh, so many anims are different. Some straight up retargeted from Stadium because 1 dev was from Stadium-Colo dev (Misaki Nakaoka, for Charmeleon and Bayleef especially)
Do note that the devs that made these models for Pokedex 3D Pro and XY are the same (Imagica Digitalscape Co., Ltd., contracted by Creatures Inc and GF). They had shifted workflow and experiences per game (some are from PokePark Dev, others newly for 3D Pro/XY). I noticed XY generally resizes claws/teeth to be bigger so that it's more visible for the low res screen, even for mons with identical poly count, while 3D Pro doesn't care as you can zoom in easily
3D Pro
XY (note, paw size is the same, but claws aren't)
Meowth's whiskers are also thicker for XY than Pokedex 3D Pro. Incidentally, he's one of the few models in 3D Pro that's lower poly
ignoring fire and smoke fx than XY (5.6K vs 5.8K)
He also has multiple versions in the leaks for XY builds