Well, I added some shading to the Voltorb and Electrode sprites (the sports ball ones), because there are not really many recognizable Pokeballs aside from the Pokeball, Great Ball, Ultra Ball and Master Ball, in my opinion. But if you don't like it, then I can change it.
Regarding Doduo, I think that the Blue bird idea will not work here, and therefore am suggesting you to use MakaTorracat's idea if she doesn't mind (this one):
I also added some shade to Exeggutor:
And completed Golduck's backsprite:
Gonna work on the rest of them now (and yes, Slowbro's a reference to The Flash).