Just to clarify a few things that you have stated EDI. If you are referring to the research that I think you are, it should be made clear that there were 2 groups within the study. The experimental group were not given shoes based on a gait analysis as you state, but instead based on foot posture/arch height as per the historical 'wet foot test' paradigm. The control group were not all given neutral shoes as you state, but instead all given stability shoes.
That aside you are absolutely right that there was no significant difference in injury rates between the 2 groups. What makes this even more statistically 'powerful' is that it was prospective in design (following them all through their basic training) and that there were approx 700 individuals in each group studied. This is huge in research terms.
It does very much suggest (and I agree with this wholeheartedly) that the current model for recommending shoes is not evidence based. I have gone on the record on this forum more than once saying that the wet foot test should be abandoned. I may have even referred to it as nonsense.
However, be careful with the other claims you have made. There is no research (currently) which suggests road running shoes "do more harm than good". There is also NO data within the scientific literature that shoes weaken feet. That should be made 100% clear for all reading. It is often stated by those with an agenda (i.e. selling more minimalist shoes) but it is not evidence based.
The neck brace analogy is also hugely inappropriate, as shoes do not immobilise feet. There is published work which clearly shows feet can and do move within a shoe.
Edited: 26/11/2012 at 19:08