Of the top five passing percentage rates for a single season, Drew is 1st and 2nd, Ken Anderson is 3rd, Steve Young 4th and Joe Montana 5th--all over 70%. This was a key stat to Walsh and the WCO as it showed passing was nearly as dependable as a handoff and more likely to gain large chunks of yardage.
The Harbaugh system is not predicated on this concept, but it certainly helps any offense. Kaepernick will improve over time, gaining touch on short passes and being more calm when throwing while being rushed. He does better on the run right now than he does from the pocket when it is collapsing around him...for obvious reasons. I don't have stats to bear that out so some may see it differenly.
The idea that he is being taught to make one read and then run just doesn't seem correct to me. I believe it is a matter of his not being able or ready to make more reads. He needs to learn this as he goes but he has probably never had to do so, his legs bailing him out whenever he needed them. That's why I believe he could re-write the record books when he learns to be more patient and use the dump offs wisely. He could absolutely dissect defenses. If he doesn't ever develop that skill it could be anyones guess why--coaching, instincts lacking, stubborness...whatever.
But I'll put my money on success...with Harbaugh and CK getting there this year or the next.