There has been some research that indicates cushioning increases the likelihood of injury. Due in part to the fact that the more the foot is cushioned then the less feedback you get from your feet. This means it is harder for your body to sense (Through Proprioception) foot position and running surface quality. Thus you do not adjust gait/speed etc accordingly and has been shown that you are more likely to trip or stumble than when you have little or no cushioning.
Also cushioning raises the foot off the running surface, increasing leverage forces applied to muscles/tendons/ligaments in your ankles and lower legs is increased. Because the cushioning foam itself is a malleable platform this reduces stability, further increasing the likelihood of injury. This is surely why Fell shoes have narrow thin, barely cushioned soles as it improves stability and reduces the risk of sprains etc on eneven surfaces.
The last point made by this research also suggested that to increase stability the body reacts by increasing the strike force in order to compress the cushioned layer sufficiently (i.e. make it thinner and stiffer) to provide a stable platform.
I guess what its really discovered is that we weren't born to wear Nikes and that we have adapted to wearing shoes with cushioning and heel lifts and motion control but at what cost? I've done quite a bit of barefooting this summer and can say that it improved my foot/ankle strength and made me run with a lighter footfall. But I guess it's not for everyone especially those who do require orthoses etc...