To weigh in with this conversation, based on many years of observation of runners, while having a neutral arch is ideal, and while shod development probably has an impact on us, we do inherit our body style. When you consider this in the equation, and considering where we developed (european descent, nigerian, etc), natural selection based on where we came from has a basis in this conversation too, since our gene pool has quite a bit to do with the type of arch, and the type of body style we develop. While I agree you can strengthen the intrinsic muscles in the foot and leg, you cannot make your body more or less symmetrical since this is inherited.
This is important because many people maintain their arches without all the exercises walking shod. Some are more symmetrical and have bodies almost designed for running while others, have more difficulties since their bodies are not as well designed for running. Many kenyans are barefoot but they have an inflexible flat arch and near perfect mechanics, ideal for running barefoot in places like Africa which developed over many years of natural selection. In Europe, where shoes were standard, you see many deviations because the needs were not the same.
Also, with all the strenthening of the arches, while the arch may improve, over time, it will again collapse because of things such as foot flare and the way the rest of the persons body is built as well as their proportions.
The point I am making is that while having an arch is biomechanically more desirable, symmetry is more important because that affects the core which affects the legs which affects the intensity of ground contact. This is where running problems come from, shod or not. Also, we need to consider the idea of cheating the system as I stated in my book Cheating Mother Nature, what you need to know to beat chronic pain. Simply explained, it is not wrong to use a minimalist shoe and then use even a minor amount of correction such as superfeet e.g. to create symmetry, which helps improve core function, reduce over and under striding and reduces injuries. In our offices, this is how we get less than perfect form runners to compete and win, even though their body style without some help may slow them down or worse, leave them open to injury.
