Weedle = Needs an animation
Pikachu
Charmeleon
Mew
Squirtle
Caterpie = Needs animation
Dratini/Dragonair = Needs Animation
Espeon = Needs a tail animation.
Pidgey = When trying to battle it, we currently have to hit it's shadow, we want to hit it's body
Milktank = In pixelmon, they are waaaay smaller than in the series or games.
Meowth = a liiiiitle too small
Nidoranfemale = Too small, even smaller than Nidoranmale
Hypno = Maybe the thing it's holding should be swinging.
Mankey
Scyther = Some kind of animation, it looks like it's posing for a picture
Poliwag = Maybe a little bigger, I think it's bigger in the series
Poliwhirl
Psyduck
Bugs: Jungle pokemon spawns inside leaves so hard to catch, Speed glitch, some pokemon that are slower than the opponent goes first anyway.
Leave a reply if you have more ideas of Pokemon Models or animations, I'll edit this if I get more information about the list of pokemon above.