Hmmm... really good thread... well, I haven't heard as many superhuman stories about O'Sensei as you guys seem to have. It doesn't surprise me, though. Someone as famous as he is bound to have some legends written about him. Further, it seems reasonable that some feats, which seen live could be considered merely remarkable, might be exaggerated to an extreme. I doubt O'Sensei wanted or needed to encourage this himself.
Having said that, I think O'Sensei did do some VERY "remarkable" things. I remember only one story, told by Kisshomaru Ueshiba, no less, of O'Sensei being caught by a number of riflemen, and, since he was convinced he was about to die, actually acheived a clarity of mind that, supposedly, let him "see" who was going to fire and when, thus allowing him to dodge the bullets. Amazing, but I doubt it was like the rooftop scene from "The Matrix." Further, we have to remember that these guys were using bolt-action rifles, and not machine guns, and may not have been great shots to begin with. Considering all of this, the feat is truly worthy of awe, respect, and amazement, but is not, in fact, "magic." I submit, in the words of Dr. Strange, that "magic is just science that hasn't been discovered yet."
Now, before all you mystics out there flame me, I'll say one more thing: I think people who think of Aikido as mere physics are engaged in a very sad pursuit indeed. You can argue all you want over what "Ki" is, or what "energy flow" is in a technique, but you can't argue that what you do is triggered by your brain, and that Aikido encourages you to make sure that what your brain demands is triggered by what your mind feels. As such, practice becomes more than just sensing where uke is standing/grabbing/punching etc. It becomes sensing, through physical connection, what uke is feeling. If that's not the soul, I don't know what is. It's not "magic" either. It's just learning to be in tune with yourself and others. I think O'Sensei understood this, and the inspiration to us all to practice that is his legacy. He was a remarkable man, but just a man nonetheless.