New experiments confirm that the radius of the proton is smaller than expected from standard theory: http://www.newscientist.com/article/dn23105-shrinking-proton-puzzle-persists-in-new-measurement.html
While we are waiting muon scattering experiment results only thing we can do, is speculate. One thing which automatically comes to my mind (besides the correctness of the experiment) is underlying theory and its correctness. If scattering results confirm the anomaly then underlying theory must be modified.
I have this particular anomaly in my todo list and I'm going to write a paper about it next year. It will be based on my pet model (ToEbi).
your question suggests that QED predicts the radius of the proton. Of course, this is more a matter of QCD with only a minor influence of QED. What is predicted by QED is the connection between Pohl's experimental data and the charge distribution of the Proton.
Apart from this caveling, I have not to contribute an idea how to solve the puzzle. It's not even on my todo list (see Kimmo's contribution).