Here's video on Warner's Corner at nfl.com, see: http://www.nfl.com/videos/nfl-network-gameday/0ap2000000128604/Warner-s-Corner-Kaepernick
Warner has been a favorite football analyst/commentator of mine (as well as xSTL team mate Marshall Faulk see: How-to-read-the-zone-read-option) so when they speak I listen. I can't watch nfl network at this time (funding issues for the past couple of years), but I do watch them every now and then on nfl.com
What makes the above video so good is Warner's breakdown of each play. There is a segment where he identify's what Kaepernick is looking at on a play action off of an option read. Kaepernick scans half the field for his one player, once he assess' the left side is not an option to pass, he quickly rotates to the right, identify's his player is open and slings a pass. This is what separates most QB's, first is the physical tools to throw a ball on a line with zip versus having to loft a ball to the right spot. The second I believe comes from great tutoring which is what Harbaugh and staff (Roman and QB coach if there is one) has done w/Kaepernick for a year and a half before unleashing him this season.
Warner goes on to identify Kaepernick great awareness to run, when no pressure or pressure exists, to the open area on the field. Having watched Kaepernick at UNR for several years, I believe this is where his college coach Ault was instrumental in having Kaepernick identify the open area and the smarts to get down prior to a tackle (or out of bounds). Long live the Pistol Offense. NFL.com has a video of Ault on Kaepernick
I just thought to mention, that 'weaker armed' QB's can also do the same thing as Kaepernick, it's just they need to have better coordination with WR. The QB's w/o the zip, will have to throw to the open spot and the WR will need to get to that open spot. For WR's I believe they would rather have the deep passes w/more loft as it allows them to run under the ball and make the catch. DBs would also rather see the lofty passes, the QBs that can throw the ball on a rope 30+ yds will always give them issues. WR's with QBs that can gun the ball, need to have better hand-eye coordination and not necessarily speed. I'll take a good hands WR over a speed WR any day of the week. And I'll take a QB with accuracy and play recognition over a QB with the physical tools. Sadly I think many coaches think they can coach up these physically gifted players, but from my observations there are very few that can teach play recognition (or where's the open spot vs this defense).
Of all the coaches in the college world that I wish had made the leap to the NFL, Urban Meyer tops the list. He had great players on his team, but we also now know he also was handicapped w/Tebow throwing ability (as well as with prior QBs). Right now, Alabama is the toast of the college world, but if you track the players from Alabama playing in the NFL, for the most part I believe they are over rated. In particular I find there LBs lack range and lack short area quickness, they are big, strong and fast, have been known to stop the run fairly well, but are deficient in defending the pass. The best out of Alabama maybe their RB's, OL and WRs. I think the NFL should pluck more WR's out of the spread systems. Well enough of this rant....