Watch any child that is learning to walk/run and they run on the balls of their feet. It isn't until we put shoes on our feet that have an elevated heal that we "learn" to walk in this heal to toe pattern. It is my opinion that an elevated shoe trains you to walk/run heal to toe and that it is not natural.
I have been very active in sports and training my whole life up until the last few years when my ankles, knees and hips have responded very negatively to my exercising (primarily running and hiking). I was introduced to the idea of barefoot running (and vibram five fingers) about 3 months ago and immediately started going barefoot around my house and yard as much as I possibly could.
About 3 weeks ago I started running in my vff kso's and am completely sold on it. My leg muscles certainly responded in much pain, but my joints have had no pain. I ran for 3 miles yesterday with no joint pain and it was great!
The impact of heal striking is something no shoe can absorb and as a result your joints must take that impact at some level. One has to think that eventually they will wear out...
The US Army has brought in a trainer that is "re-training" their personnel how to run properly and has greatly reduced injuries and increased the pace at which the soldiers can run. Check this article out for more information. http://www.army.mil/-news/2009/06/26/23546-new-running-technique-strikes-a-pose/
Living in the Minnesota Tundra, I will not venture out into actual barefoot running until next spring, but I really believe that if you tune into what your feet are communicating to you, they will help you learn how to run properly. Ken Saxton has a lot of good information on his website about barefoot running as well. http://runningbarefoot.org/