The time is now for Colin Kaepernick in San Francisco

Jake Roth, USA Today Sports

The San Francisco 49ers already find themselves at a crossroads just two games into the Chip Kelly era.

It’s not because they are playing horrible football. Here’s a team that will enter Week 3 in first place in the NFC West (tiebreaker). It dominated the Los Angeles Rams to the tune of 28-0 in the season opener before dropping a road game to the Carolina Panthers on Sunday.

That was a game that actually saw San Francisco within one score midway through the fourth quarter.

We’re seeing a much more competitive product than the version San Francisco trotted out there during the second half of the 2014 season and all of last year.

There is, however, one major weak link here. It’s not the coaching. It’s not the offensive line. And despite allowing 500-plus yards to Carolina on Sunday, it’s not the defense.

Instead, it comes in the form of former Jacksonville Jaguars top-10 bust Blaine Gabbert, who has proven he’s not capable of holding down a starting job in the NFL. This was evident in Jacksonville and has come back in droves over the first two games of the 2016 season.

At this point, it’s hard for Kelly to justify continuing to throw Gabbert out there with most other aspects of the team performing well.

Despite being hit just five times and sacked a total of two times in as many games, Gabbert’s stats tell us a story of  bad quarterback play. Potentially the most inept quarterback play in the NFL today.

He’s doing this all within the confines of a Kelly-led offensive system that’s been quarterback friendly in the past.

This is with the likes of Nick Foles, Mark Sanchez, Matt Barkley and Sam Bradford starting games under Kelly in Philadelphia.

Needless to say, it’s quite the accomplishment for Gabbert to perform at such a significantly lower level than these four marginal quarterbacks.

For his part, Kelly seems to be toeing a specific line when it comes to the 49ers’ quarterback situation.

Kelly went on to indicate that the entire roster is going through competition when asked if there was one surrounding the quarterback position.

What we do know is that Colin Kaepernick is still regaining his arm strength after being sidelined for the first three games of the preseason with a dead arm. That could delay a potential quarterback switch for a couple weeks.

We also know that this 49ers team is much more competitive than we’ve seen in the recent past. It’s also 1-1 heading into a big Week 3 outing against the Seahawks in Seattle. Considering how much Kaepernick has struggled in the Pacific Northwest, that’s probably not the optimal position to put him in.

Despite Gabbert’s lack of success through two games, San Francisco’s offense as a whole has picked up under Kelly. It is averaging 22 first downs and 27.5 points per game thus far this season.

For comparison’s sake, San Francisco reached both plateaus once in its previous 34 games prior to Kelly’s arrival. That speaks to the coach’s system and the underrated ability of others on offense not under center.

None of this is to say that Kaepernick would immediately return to 2012 form when he led San Francisco to the Super Bowl. We’re so far removed from seeing the embattled quarterback play at that level, it’s almost like it never happened.

Even then, it must be noted that Kaepernick’s struggles over the past two seasons were not all his own. San Francisco’s offensive scheme was a complete disaster last season.

His offensive line failed him at every turn. And in reality, the latter part of Jim Harbaugh’s tenure in 2014 was filled with questionable play-calling from the now unemployed Greg Roman.

This isn’t to make excuses for Kaepernick. He regressed each of the past two seasons —a regression we’ve rarely seen from a quarterback in modern NFL history.

The only question that needs to be asked here is whether Kaepernick boasts more upside in Kelly’s system than Gabbert? If the answer to this question is a yes, the first-year head coach must make the move.

He must do so while muting the outside noise of the anthem protest controversy.

He must do so while fully acknowledging that he might be going away from what the 49ers’ brass wants him to do (more on that here).

In order to move forward as the actual coach of this team, Kelly must make it known that he’s deciding what happens on the field come Sunday. If that doesn’t happen, this is going to be no different than his short-lived tenure in Philadelphia.

It could also waste a golden opportunity for the 49ers themselves to surprise the football world and progress at a rapid rate this season.

Gabbert isn’t the answer. Maybe it’s finally time to see if Kaepernick has anything left. What do the 49ers have to lose from making this switch? That’s the question Kelly must now ask himself.