First post is updated; removed the Pokemon I did from the list, image is updated, and marked a few more Pokemon for colour correction... maybe I'll use a different background colour for those. Eh, later.
Calvius- I took a look at the edits you made, and they don't look bad but there's a different problem. It looks like you used some kind of blending tool on photoshop or something? The problem with doing that is it results in a loooot of different colours (by colours here I mean specific shades of brightness/saturation/hue) which becomes really messy and impossible for sprites to efficiently work with. Like, in Quilladin's tail alone there were around fifteen different colour shades x,x