To be honest, I think Pokemonatoms is ignoring all of your criticism. He hasn't even tried the popular suggestion to work with official sprites and play around with them seeing as he went off and did a Ghost fakemon.
Anyways..Paint.NET is actually a program similar to GIMP. I never used it before for graphics or pixel art, so I'm not very experienced or familiar with the program.
(You manually recolour a sprite, pixel by pixel? o__o)