That's not too bad... I think it just needs a bit of cleaning up. Specifically, the outlines around the feet, both facings, and then the pixelation shading around the tail as a whole on the back sprite and very tip of the tail on the front.
Poliwags look great; I'll put those in once we have matching evos
Muk looks good; I'll put that in.
With Sandshrew, can we get more contrast in the shades of blue? As it is we're losing the definition of its scales.
Sandslash... is a bit better, but are those colour shades on the same actual colour? Could we make the 'spikes' a bit darker than the rest of its body? I know that's not a sonic thing but it'd look a bit truer to Sandslash.
With Ponyta, go with whatever the original sprite is.
I'm not sure how I feel about Kabuto's eyes. Try using a darker colour on their outline so they blend in? If that looks weird, then at least make them match that red.
I personally like the red one a bit more but either is good. How about others?
Machop looks pretty wicked, I'm not gonna lie. However, I'm a bit hesitant to go on dramatically changing the shape of something for what's officially just supposed to be some colouration differences. Now granted, we are taking some creative liberties here, but... I dunno, what do others think? Do you think it would be jarring for a shiny Pokemon to have its head like that even if it is for a shiny theme?
I like this Machamp colouration better so I have it quoted here. However, I think the shades could contrast just a bit more, (towards darker). Also, it's done pretty well on Machop but there are some places where its wounds could be blended in better using darker shades.