I prefer using shoes. The "barefoot is superior" bunch are silly- just because you run with shoes doesn't mean you have to run the wrong style.
As for the long distance running adaptation, my hypothesis is we might have evolved that not mainly because of persistent hunting but because of war. There's not really much selection pressure for persistent hunting if you are a social animal (like humans and apes) you can hunt very successfully in groups - lions, hyenas, wolves, dogs, apes etc do it.
In contrast war could have produced rather significant selection pressures. In human-human wars, the predator and prey are the same species- whatever big advantage you have is likely to be in the next generation of survivors. Being able to run away from dozens of persistent enemies till you find a hiding place or till the sun sets keeps your genes alive. In contrast being able to sprint at 80kph for a minute when the enemy can also sprint at 80kph for a minute doesn't help much with your survival when there are many enemies. Being able to run long distances to attack an enemy or carry messages is also helpful.