First let me state that I believe the position I've taken in the past on this issue on this site is that I am NOT anti barefoot running. However, I believe that realistically this is not a form of running that is going to be beneficial to all runners, and will result in some potential serious injuries to many.
I think that there is no doubt that if removing the motion control, padding, etc., you will certainly have a greater tactile feel and greater proprioception. You will naturally be able to build up muscles that are being used instead of relying on the actual "shoe".
I also know and respect Dr. Whitney, but I think that in actuality, the jury is still out, since this new trend has not really been around long enough to see the full benefits or the full potential problems. Yes, I know that barefoot/minimalist style running has been around a long time, but not among the general public and not with the gaining popularity it has had recently.
So the bottom line is that there will be many who will benefit from this style of running and some who will probably suffer some injuries, and hopefully those who are not comfortable with this style will realize early enough to prevent serious injury and resume to the style that suits them best.
Do whatever works for YOU, just be smart enough to know if it's helping you and that you're not just following a trend.