I agree that overbuilt shoes can promote poor mechanics/gait.
But running barefoot/minimalist never necessarily made anyone a better runner overnight. The continuous cycle of training followed by recovery is what allows for better performance.
Better mechanics certainly can help with running economy and efficiency but barefoot running is not for everyone.
What of the things that upsets me about McDougall's "born to run" is the lack of emphasis he places on weight and their relationship to injury. He mainly targets shoes as the primary culprit for more running injuries but he never really considers weight to be part of the issue.
When he was actually having chronic injuries he weighed somewhere between 220-240 lbs and was running in motion control shoes. That's a recipe for disaster.
Barefoot running/minimalism doesn't guarantee you will have no injury. I see the main reasons why most new runners(recreation joggers) get injured is because
1. Immediately enter a structured training program for an even that doesn't allow enough time for adaption/full recovery.
2. Being overweight adds stress to the joints/ligaments.
3. Poor shoe construction(heavy and stiff) creates bad gait and poor foot landing.
4. Lack of patience. Running is physically demanding and it makes you sore its supposed to hurt your body a little bit. You're asking your body to do a lot.