Monofilament thread is great, but only if you use the right type and brand. It would not usually be used for hand applique because it's hard to see and control; it is a boon to machine applique, however. I learned about it from Harriet Hargrave's wonderful book on machine applique (also took a course with her during which we quilted with monofilament).
The only type of monofilament thread I will use is YLI. This thread is .003 mm thick, similar in thickness to very fine hair. It does not create "pokies", and the feel of it in a finished quilt is not different from cotton thread; you just don't notice it. It does not break in the washer or dryer.
You would not want to use monofilament for satin stitch applique, but I am assuming you are planning on using a machine blind stitch for the applique.
If you are really deadset against using monofilament, some people substitute silk thread for blind-stitch machine applique.