This explanation is less elegant because it requires different laws of physics in the matrix real world than our world. "a direct neuro link to the machines" doesn't do anything to explain why neo has telekinetic abilities in the "real" world.
http://www.youtube.com/watch?v=JYawJGlEh3k
His powers don't work on the flesh-and-blood Bane/Smith. He can't swipe the knife away from Trinity's neck at a distance. He can't easily beat Bane/Smith in a fistfight. The best he gets is to see Smith's machine form after being blinded.
All of his powers shown in the real world are against machines, never flesh-and-blood humans.