The most plausible scenario to me, as mentioned above, has to be that it's pertaining to a Pokémon following you around, chiefly the leader of your current active team. Multiple times through the game, NPCs reference the leader of your time by name as if it was there in the cutscene, but it's not there. Like "Your Primarina looks so happy to be with you" but it's not there so how the NPCs can tell? Plus, it would be interesting to see if other NPC Pokémon models found in towns or houses etc are just as low poly as those that have walking animations. Also, the fact that they have animations for both walking and running seems to me like just another hint that those Pokémon were meant to follow you around. But maybe they just ran out of time or it caused minor slowdowns in certains areas on older 3DS models, and they prefered performance to extra details, who knows?