Unfortunately, many components of the conventional running shoe was found to literally tear away at the functional strength of the arch in ways that causes long-term damage, including collapsed arches and chronic plantar fasciitis as compared with running barefoot or in minimalist (barefoot-like) shoes. 
Sadly, cushioned running shoes do not prevent injury because according to extensive research cushioned running shoes dramatically alter joint mechanics (i.e. causing heel striking, over-striding and over-pronation) that accounts for all the impacts that cause injuries, especially servere injury, such as long bone and chronic muscle injuries. Conversly, running barefoot or in minimalist shoes enhances neuromuscular programming of a more controlled forefoot strike, while pushing the rest of your stride mechanics in a more functional direction, making you far less prone to all injuries.
Barefoot running was found to be faster for many reasons. For one, the lightness factor reduces the cost of transport of the leg at each step. Secondly, barefoot running engages a forefoot strike which in turn engages the mechanics that perfectly matches the function of the elastic structures of the lower leg. This results in a stride that’s more elastically-powered which greatly reduces the need for costly muscle demands.
The flatter your running shoes, the less you run with lopsided and mechanical imbalances because you are better at connecting properly on your forefoot, whereas running shoes with a thick cushioned heel are a mechanical interference that continuously undermines your forefoot strike control.
The more time you spend walking, running or working-out barefoot or in minimalist shoes, the more balanced you’ll be when you run in cushier shoes. This is because the more your feet can feel the ground, the stronger the electrical outputs in our neuromotor circuits become, the better your reflexes will be at keeping you more stable in cushioned shoes!
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