first of all mc: Running Shoes as Single Factor Thinking
This is a post about Shoes not as evil, but as it seems a Great Feat of Misdirection. It's a wee bit about our biases towards single factor solutions for complex problems, and the arguments we will have around the Chosen Factor rather than pulling up and back to consider the wider view.
Then Steven Low has updated his fascinating post: Shoes, Sitting and Lower Body Dysfunctions
It is a thorough analysis of how many of the common orthopedic problems today arise from shoes and sitting, how to evaluate their development, and finally a look at how to implement prehabilitation or rehabilitative protocol to improve their condition. I sincerely wish that you will read through the whole thing even though it is a monster. I promise you will come out with a new outlook on this topic.