Hi. I saw your question a few days ago and have been tring to find a spare moment to post a few tips about face embroidery. These work for me!
I find that 6 strand floss works best on flat surfaces, such as cotton knit or broadcloth doll skin. I like to separate the floss strands in half, so that I have 2 strings-3 strands each, and I like a length of about 22 inches long, for a 16" doll head. I take small piece of all natural beeswax and run the strands through the wax a couple of times to coat it well. Then, using the satin stitch, I embroider an eye with each string, counting the number of stitches so that they are equal on each, and making sure that the eyes match. I use the same method for the mouth, except that I use the 6 strands whole. The wax really helps to control the floss and gives a nice even satin stitch which lays flat to the surface and covers well.
I have found that Pearl cotton embroidery thread works best for fuzzy or furry fabrics. It is more 3 dimensional, and shows up better against the pile. It has a nice sheen, and comes in at least three different thicknesses. On large items, or longer pile, the thicker I go with the thread. For small plushies, or felt animals, I usually use a size '8'. Larger toys over 10" such as Teddy Bears and Rabbits, I use a '5' or even a '3' on very long pile for noses and mouths.(The higher numbers mean thinner thread.) On these furry items, I use a piece of 1.5mm felt cut to shape and satin stitch over the felt. The felt keeps the pile from coming through the stitching and gives the nose a plump 3D effect. Sometimes I carefully trim away the pile on the area to be embroidered. I always hand embroider the face last, after sewing and stuffing is done, and I never wax the thread when embroidering furry items.
Machine embroidery is done while the pieces are flat, before sewing, but hand embroidery has the advantage of being done after construction, so that you have the most accurate and pleasing placement of the features. HTH