Ballistic gel tests show that the 40 cal bullets punch a larger hole, penetrate as far or farther than the 9mm, and create a much larger wound channel than the 9mm. That is certainly not always the case, as some 9mm rounds will outpenetrate the .40, even using rounds from the same batch during the test. The results will likely vary enough to "wash out" against each other. Compare different rounds and the results are even less certain. Agree?
Further, heavier bullets carry more momentum and kinetic energy and therefore do better when striking bone.That is making the assumption that a 9mm needs any help penetrating any bone in the human body, which it does not. Furthermore, there is nothing in the human body that will hinder the 9mm, but allow the .40 to pass. If anything, the bullet SD will determine what will do better, and that is caliber independent.
Compare the 124grn 9mm with the 165grn 40s&w and the 147grn 9mm with the 180grn 40s&w. While they penetrate about the same distance, look at the difference in wound channels. Note that the 40s&w bullets of both weights create significantly larger wound channels than their equivalent 9mm bullets. Further, note that this test doesn't even bother with the 115grn 9mm bullets. Wound channel causes organ and tissue disruption which generates more blood loss and faster incapacitation.As was said above, the wound channel is insignificant in incapacitation. It is not enough to be a fight-stopper, and the adrenaline rush of fight-or-flight will counteract the small issues caused by the vascular damage and bruising. The person who posed the idea of shooting a 5-gal bucket of water is on the right track, but I'll take it a step further and say a 5-gal bucket filled with small diameter rubber hoses and sponge material, all containing the water. It would be even less of a difference in fluid loss.
In addition, extensive FBI testing has repeatedly demonstrated the advantage of the 40s&w over the 9mm notwithstanding the 9mm crowd's fancy talking around the results. Care to cite any of it? I sure can't, but I didn't make the claim. What I have seen from the FBI is more inline with the thought that the difference is minimal. This is evident with their reports on "stopping power" and bullet effectiveness.