@Bioshock: Oh ok, I wasn’t sure if you knew so I wanted to make sure I’m not assuming your level of knowledge in the programs just safer to explain what it is. XD
You are absolutely correct, if the style was pure pixel art then you would be only allowed to use the pixel brush. Because we do a style called soft toolshading the process only requires the outline to be done with a pencil to give that pixelated edge look and inside is done with a soft brush as you explained.
The sketch step can be done as you had explained, you can simply trace a cleaner version on your base layer but simply making the opacity lower so you can see your sketch under. That is not a wrong process, using my original sketch is just my process so you are welcome to alter it to what’s easiest or best for you.
There are some pixel artists that do work like you mentioned, each hue has a new layer. Personally I feel like it’s harder to blend the shades because brushes tend to have a blending aspect to them so they would grab from the color that is laid out and mix with the one you are laying down so give a more soft transition. But if working on different layers is better for you and it’s the way you work by all means. At the end of the day the final result is what matters, not necessarily the process of the artist.
In terms of consistency, you are very correct by matching hues to the sites items. I always say that make sure that the majority of the item is the base color. So if say you do a lot of shading on the item and the base color is barely visible your item will not match with other items. That’s why you have to be careful of over shading and putting too much detail when shading. If you feel like you’ve over done it then I would just go back in with base hue and gently bring it back into the item where you feel like the shading has gotten too dark.