Has research into the aerodynamic properties of non-smooth surfaces suggested any promising directions for future aircraft design?
Non-smooth surfaces are already used, particularly in some Military Aircraft. If you've ever run your hand down the fuselage of an FA-18 Hornet you will find the surface is quite rough, much like the skin of a shark. At lower speeds very little is achieved, however at higher speeds small bubbles of air buildup in the indentations of the skin thereby creating an extremely slippery surface.  

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I'm certain my terminology is not correct, sorry about that. I would have put this all into comment, but I'm not allowed yet.