As Kelly plotted his next NFL stop, per NFL Media Insider Ian Rapoport, he was hatching plans to sign or trade for Kaepenerick as his next quarterback project.
Although Kaepernick's early November benching sparked speculation that his days in San Francisco were numbered, Rapoport reports general manager Trent Baalke sat down with the quarterback to extend an olive branch prior to the season's end.
Kelly's innovative offense didn't realize its full potential in Philadelphia over the past two seasons because his quarterbacks lacked the running ability to stress defenses at the mesh point.
"What Kelly did not have in Philadelphia was a quarterback that could handle the second part of the zone read," NFL Media analyst Mike Mayock outlined Thursday. "Everything was a zone give, not a zone keep. And they had to do an awful lot of different things to work around the fact that they didn't have an athletic quarterback."
The issue goes beyond the quarterback to the ground attack. If defenses don't fear the quarterback as a threat to take off and run, they will sell out to stop the tailback.
The Kelly-Kaepernick hiring should have a symbiotic effect in that regard.
While Kaepernick's ability to run the read-option is tailor-made for Kelly, the 49ers' new offensive system offers a Kap-friendly passing element that once inspired Around The NFL's Gregg Rosenthal to label the scheme quarterback-proof.
"I think for Colin Kaepernick's career, it's one of the best things that could have happened for him," Mayock added. "... It's very quarterback-friendly as far as the pass game is concerned. There are a lot of fairly simple reads and I think Kaepernick can pick it up very quickly and I think you'll probably see a very efficient and very effective Colin Kaepernick next year."
If that sounds familiar, it's because Jim Harbaugh and Greg Roman allowed Kaepernick to operate in a similar fashion en route to Super Bowl XLVII.
That formula changed once the 49ers rewarded Kaepernick with a franchise-quarterback contract in the offseason of 2014. Thereafter, the emphasis on developing Kaepernick as a progression pocket passer backfired. As his surrounding talent disintegrated, Kaepernick struggled with field vision, decision making, accuracy and touch.
Kelly offers Kaepernick a chance to succeed with quick, simplified "half-field, high-low type of reads," as Mayock explained.
The opportunity is there for Kaepernick to recapture the dual-threat form that once moved ESPN's Ron Jaworski to rave that Kap could develop into "one of the greatest quarterbacks ever."
Dual-threat quarterbacks stress defenses as a runner and as a passer. The premier NFL quarterbacks, however, are triple threats willing to exhaust plays and beat defenses from the pocket week-in and week-out.