Variable exhaust timing is more likely responsible for most of the gains. There isn't much room to improve on burning more fuel on a modern engine.
EDIT: one more technology that has been proven to work is electrostatic fuel injectors
http://www.sae.org/technical/papers/2000-01-2041
If 2 to 3 percent improvement in mileage were possible from better atomization alone they would be doing already.