Colin Kaepernick will improve while Russell Wilson will regress.

I am a ‘Niners fan and I am very biased. 

In the second half of last season I was frustrated with how natural Wilson looked as a quarterback, especially compared to Kaepernick; who for all of his ungodly natural gifts looked stiff and slow to react.  I watched Wilson throw catchable passes to where a receiver was going to be open, and ground my teeth as Kaepernick beamed lasers into quickly closing windows after his receiver had made his move.   I marveled at how Wilson would expertly bait an incoming rusher before escaping the pocket, yet Kaepernick seemed shocked when a defensive end was able to catch him.  Kaepernick often struggled to get the a play called, or  an audible, where Wilson and the Seahawks seamed unimaginably prepared.  To make the comparison more lopsided Seattle has added more weapons around Wilson where Kaepernick lost his favorite target.  Yet, some of those failings of Kaepernick's are exactly why I expect him to close the gap between him and Wilson next season.  (All of that is heavily subjected to perception bias, a statistical analysis could very well prove that the opposite was true, but as a fan this was my perception).  

Kaepernick is a nearly unique physical specimen, with prototypical size, throwing power and accuracy, combined with unnatural speed and power at the quarterback position (Cam Newton is the only other quarterback with all of the same tools, Wilson lacks the size and throwing power, Luck and many others lack the speed, Griffin and Vick lack the strength).  Kaepernick used those tools to compensate when he did not have the read of a play, or time to get the correct set play.  Most quarterbacks do not have that luxury.  Last year I feared that in spite of all of the great plays Kaepernick was not a natural quarterback, and that he would plateau early, like so many physically gifted athletes do at the quarterback position.  

Two realizations changed my thinking on the matter.  

Kap Excercises his Brain:  An ESPN Radio commentator (Colin Cowherd I think) shared that Kaepernick was encyclopedic in his ability to ingest and apply information.  This started me on a quest to find stories of his work on the mental side of the game, and I was very impressed.  Kaepernick is well known for intense exercise regimen, and his mental exercise is just as intense and consistent.  Kap is constantly quizzing his teammates on plays, formations, audibles, the depth of routs, the blocking protections, and adjustments to defenses they will face.  It is one thing to know how a play goes, and another thing entirely to implement that knowledge at game speed, but those mental reps are well regarded by coaches and successful veterans as being key to success.  

Practice Time Matters:  If Kaepernick works this hard mentally, why was he still so raw?  For the first time Kaepernick will have a preseason, OTA’s and Mini-camps as QB1.  This will give him hundreds of  situational practice plays with the starting roster that he did not have as QB2.  Those extra reps will reduce the clock management failings (for examples look at the redzone in the 2013 Superbowl) and those hundreds of additional practice throws (helping him to master his timing with receiver) will reduce problem of forcing passes though closing windows.  

Why Wilson Will Regress:  Every defensive coordinator has seen footage of the read option, and they are
preparing their defenses for it. The defensive ends will be prepared to keep contain on both Wilson and Kaepernick, but with his size and power I expect Kaepernick to thrive from the pocket.  It will be much harder for Wilson to see and throw over the mass in front of him (but it can be done, and he will do it a lot, but over the course of a season there will be key plays where he cannot see a LB, or a DT bats down a pass, or there simply is not a throwing available).   

In short, next year the league will have time to prepare for Wilson, but Kaepernick will have time to prepare for the league. 

I am wrong if:  If Kaepernick throws more interceptions than Wilson, or if it is subjectively clear that Wilson is still the superior QB, then Kaepernick has not closed the gap. 

Odds I am wrong:  55%, and that is a 5% chance that Kaepernick does not improve compared to a 50% chance that Wilson does not regress like I believe he will, or that his new weapons offset that regression, or that defenses do not yet have the tools or schemes to effectively limit the read option or hold outside contain against Wilson.