I'm going to argue for at least three catagories of flys, based on thier construction.

1. Dry flys that float high on the water, such as a catskills pattern or a elk hair caddis.

2. Standard sub-surface flies, streamers, nymphs, bead heads and the like.

3. Flies designed to sit in the film, like a serendipity emerger pattern or a no-hackle dun.

Certainly you might cross catagories and use a dry fly for fishing wet, or put a spot of floatant on a hare's ear to keep it in the film.

I think the design of the fly is effected by it's taget catagory. For example a nymph to be fished deep will be tied on a heavy wire hook, might have a lead underbody or a bead head. A dry high floating bug would use water repelent muskrat dubbing and a light wire hook and your best dry fly hackles. A surface film style fly often combines the materials used on a traditional nymph, but light wire hooks and possibly even a dubbing ball or light hackle to give a little floatation.