I think you need to have better palette choices as well, for example, your Groudon. You could make the colour for its eyes more useful by adding it on for shading it. Yellow may look like it doesn't fit, but it will.
Like GFA said, the Shiny Torchic's colour is a horrible inverse, why would the highlights be darker than it's base colour(you used orange as a highlight and light orange as a base colour)? Surely you should use a brighter orange or white even.
And like The 100 Mega Shock said, you are overusing the dithering method and style. For example,Grotle's bush would look more impressive if you shaded it like the current sprites, it'll make it look more natural.