And keeping Kaepernick is the 49ers’ best chance, at least in the short term, to have the sort of quarterback Kelly needs to make his fast-break offense work.

Multiple reports, the first by the league-owned NFL Network, said Thursday that Kaepernick’s representatives have asked for permission from the 49ers to seek a trade. That came after 49ers officials said this week at the NFL scouting combine that they expect Kaepernick to be on their roster and have been given no indication he wants to leave.

It’s not like the once-proud 49ers have been known in recent years for making wise choices. Jed York, the team’s chief executive officer, and General Manager Trent Baalke failed to make things work with Jim Harbaugh, the abrasive-but-successful coach who restored some of the franchise’s glorious past with three straight trips to the NFC title game and a Super Bowl appearance, then promoted Jim Tomsula to replace Harbaugh and dismissed him after one season.

AD

AD

Now the Niners are counting on Kelly to be the coach that he was for two seasons in Philadelphia before being undone in Year 3 by his own ill-fated roster decisions when the Eagles handed control over all player-related decisions to him.

Kelly needs a quarterback. It seems unlikely that Blaine Gabbert, who took over for Kaepernick as the starter this past season, is the long-term answer. The 49ers have the No. 7 overall pick in the NFL draft and could seek their quarterback solution that way. But draft analysts say the best quarterback likely to be still available at that point in the draft, Paxton Lynch of Memphis, probably won’t be ready to be a productive starter as a rookie.

Kelly once coached a 27-touchdown, two-interception season out of Nick Foles in Philadelphia. Maybe he can get the best out of Kaepernick. Maybe he can’t. But at least there is talent there, and nursing Kaepernick back to something resembling his best would give the 49ers a better quarterback than they would have by starting Gabbert or relying on a rookie.

AD

AD

From Kaepernick’s perspective, there are other quarterback-needy teams out there. The New York Jets have been mentioned prominently as a potential landing spot for him with last season’s starter, Ryan Fitzpatrick, eligible for free agency. But would playing for the Jets give Kaepernick a better chance to reassemble his career than playing for Kelly in San Francisco? Kaepernick might be wise to take a close look at what playing in Kelly’s offense might do for him.

Kaepernick and the 49ers need each other right now. If both sides don’t realize that, they could end up making a damaging mistake.