I remember somebody going through the models in a video back around when the games released. He compared values across several Pokémon, and while some do have actual alterations, others don't. As an example, Sylveon has one rogue triangle removed, basically nothing. Pikachu's cheeks are properly modeled rather than just being textures, but the rest of the model is identical. A number of Pokédex are basically identical. But suffice it to say that many of the changes are not major or noteworthy. I wouldn't call them justification for the outright removal of Pokémon. The textures are a bigger deal since Pokémon with low resolution textures would stand out on an HD platform (Masters has this problem when you look at the Pokémon in comparison to the Trainers), but I'm 99% sure that industry practice is to make textures at a high resolution and then downscale them to what's appropriately for the platform. They should have hi-res textures for the 3DS models.
