[I'm sure more details are desired, but I already posted two pictures with the palette I'm talking about, and I don't want to fill up this thread with posts about it. If and when I have something I think is ready to show, I'll post it in another thread and explain it there.]
You are using two of the more grayish blues to double as shades of gray and of blue. You probably swapped them for the similar grays and put Knuckles' pinkish shades in their place, as they are the only palette entries that are 'safe' because of Super Sonic. And shunting off the green to another palette line means you may have edited Knuckles art so that the socks are in separate tiles which are shunted into a different palette line.
While I will look into doing something similar (back to sed for me), I will still keep the S3&K sprites because I prefer them to the S2 ones.