Decide on what colours you are going to use for the skin. There are many other good tutorials that explain this in great detail, so I'll just give a quick explanation as to how I go about this. When making a colour darker, reduce the value (how light something is) and shift the hue one that is darker, and when making a colour lighter, do the opposite. You can choose whether you want to increase or decrease the saturation (how bright a colour is) as a colour gets darker, but is is usually a better idea to gain saturation. The black on my Zygarde skinis a good example of colours getting more saturated as they get lighter.

I usually create 4 shades per colour, and I always put the palette in the top left, for consistency.

Using the colours you just chose, draw on the basic outline of what the skin is going to look like. Some may say that it is now finished, but you've barely started.

Covert the mouth and eyes into something a bit more realistic by moving the pupils and mouth onto the hat layer. Re-colour the 'jaw' on the hat layer to the skin colour, and add a pixel onto either side. Remove the pupils from the eyes on the head.
Also, I put the tips of the ears onto the hat layer, because YOLO.

...and shade. I usually shade the head with a top-down light source. I can't really explain how I shade, I just put the colours where I feel they should go.

...and repeat. I usually shade the arms as if there is a light source towards the outside of the arms, to the left and right of the skin.

My signature hand style that I created myself. I like it because it is shaped like a fist, that is positioned to punch things, in stead of tickle things. It also doesn't have a thumb that is as wide as the arm.
Here it is, as well as a sort of graphical explanation.

...and in 3D

More shading. Make the clothing really tight, so that the muscles pop out, because otherwise it would look really flat.

To help make the chest and shoulder blades 'pop', don't put borders around the edge of the upper body, as the arms will make up the border.
For example:

Don't worry, this is probably the easiest step. Shade the sides, top and bottom of the body. These areas are usually coverred up, so put them in shadow.

I noticed that the red and green didn't go very well together, so I changed them.

I tend to try and make it look like the lower leg is larger on the back, and the upper leg is larger at the front. Probably not perfect anatomy, but oh well, it looks nice.