One thing that stands out to me with Pokemon's visuals are how out of place the Pokemon feel in their own game. We have Pokemon that have "fur" or "scales" but no fur or scale textures, BUT they are in environments that have textures, bad looking textures, but they're there. Be consistent. They really need to go with a Cell Shaded look, but they won't because it would be to much work.
BTW here's Pokken, A Wii U game that got it right.








