Part of the problem is a lot of pokemon weren’t designed to live in a world, just be a sprite on a battle screen. It also got more egregious in later titles, but there’s always been some problematic pokemon. So not only do you have to make a ton of models, you have to fudge the scales a lot to make Pidgey vs Onix look remotely good. There’s really no way to make a decent looking game without drastically reducing the scope like pokemon snap did.