Kaepernick also in 2012 was dominantly a beneficiary of the system in place in San Francisco for Jim Harbaugh's read-option offence, which was made obsolete practically in the NFL in 2013 after a rule change in the offseason allowed for the quarterback in such a position handing off the ball to also be clobbered as opposed to before only if he still had the ball as a runner or otherwise. And perhaps you recall earlier in the season that Alex Smith, since that season the starter in Kansas City, was running that offense before Kaepernick and his "hot hand" took over.
All defensive players took note after the rule change that they would play the read-option offense to clobber both the quarterback and the running back on every play no matter what was going to be done with the ball. Before in 2012 they were often clobbering the QB in a read option offense anyway and did draw some penalties, but now there were no penalties to be had given the rule change.
You might recall that also Robert Griffin III and Russell Wilson also thrived in that 2012 season. Wilson of course has since adapted his game as a passer. The other two did not obviously.
As Warren Sapp as a guest on local homer sports radio at the time when I was in Tampa Bay explained, and this was before his gaffes in life of course, no offensive coordinator who in his right mind wanted to keep his job was going to call such plays any more given the increased risk of injury.
I'm of the opinion that the NFL establishment owners wanted the change also given the legal situation with the lawsuit of former players, for any rule changes that discouraged as much hard hitting were and still are en vogue.
About three years ago here I did a post on NFL QBs who I thought had the game for a CFL offence so as to shed better light on all the dubious claims, often from my fellow Americans, that any given NFL QB could play in the CFL. The answer more often than not in my opinion was no. Those QBs without consistent passing accuracy of 60% in the NFL (or in NCAA college football for that matter!) are not going to make it with one less down in the CFL out of the shotgun even with the defensive line one yard off the ball plus the wider field. And those who are merely drop-back passers would not make it necessarily if they can't throw well on the run or do not have good mobility, for those guys can't get away with just chucking the ball away as much like they do often to avoid sacks in the NFL given one down. Some of the latter are fine starting NFL QBs mind you.
Kaepernick was one of the names on which I was 50/50 back then though now would be pessimistic. His core problem is throwing accuracy, but when in the past he was able to throw also on the run he was deadly and no doubt he does still possess a very strong arm and is still fast.
Might Kaepernick thrive in a more open offense on a wider field that rewards quarterback mobility to run and to throw more than does the NFL on its narrower field?
It's a long shot, but we shall see if some team takes a chance on Kaepernick.