Oooh, so that was that thing on the hair.... it's hair...
I think that you are mixing two different styles of drawing. While you keep a dramatic total black "I'm-such-a-badass-ninja" shading on his face, you changed the "representation of shadow" to a more, mmm, soften shading. In the wole game you shouldn't change the style, it's has to be constant in order to maintain some sort of identity. While doing some difference between the style on the background and the animated sprites is not just tolerable but some times even a good choice, such must don't be done in a single indivisible character.
Also, the total black shading don't seem to be a good choice for pixel art, at least on that scale. Check some post & comments around here, or even visit some other webs about pixel art, and you maybe see that usually people do the shading by mixing the original color to yellow for brightest areas and to violet or purple for the darkest ones (it's a bit more complicated than that, so go check if you are interested).
By the other hand... what about that foot? I only think that he haves one leg taller than other, wich is not necessarily bad, as he could be a ninja with all his life, since he was trained, complicated because of his imbalance, then the last weekend on the temple his partners make him a really bad joke about that, and now is soo madly mad that his face turns chillingly shaded and decides to kill everybody, even his own master...