In trying to determine who is "winning" the debate between neo-Darwinists and Michael Behe, we should ask ourselves who has the burden of proof? Is it up to Behe to prove that neo-Darwinism is wrong? Or is it up to the neo-Darwinists to prove that they are right?
One could argue that Behe has the burden of proof. After all, neo-Darwinism is the the consensus view in biology, with few scientists seeing any strong reasons to give it up.
I suggest that recent discoveries have shifted the burden. There is a famous quotation from Bruce Alberts, former president of the National Academy of Sciences:
"We have always underestimated cells. … The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. … Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts."
(Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92(February 8, 1998): 291)
When he said that we have always underestimated cells, he was referring to a time after the Modern Synthesis, but before we were able to study the inner workings of the cell.
Behe tells us that "the great majority of proteins in the cell work in complexes of six or more."
Most biologists claim that the origin of these complexes can be explained by neo-Darwinism. Perhaps they are right. But we would like some indication that the great majority of protein complexes, which are composed of six or more proteins, actually evolved from simpler complexes. Which ones? And how? Neo-Darwinism needn't explain the evolution of every protein complex. But I would think at least a half-dozen or so should do, just so we know that it can explain them.
I may be mistaken, but I don't think this has been done, yet. Until it is done, I suggest we withhold assent from neo-Darwinism.