It may not be practical for some people,but you forget the core target audience for Pokémon games: Kids. Most kids, especially in Japan, don't just sit at home online. They interact with their friends to play games and THIS is what they're pushing. It's illogical to just scrap that to put it on a home console, cutting out a good portion of why kids actually play the game
I agree, and thankfully the models are used as a standard for Pokémon games now (the same models used for spin-offs, arcade games etc.). The Noivern model you posted is of the same quality as the redone models for Pokédex 3D Pro so it shouldn't be too hard. Minimal effort in the model department. All they've done for XY is add a special texture on it to make it akin to Sugimori's style
No one is asking them to scrap portable Pokemon.