Why did Chip Kelly wait so long to start Colin Kaepernick?

Blaine Gabbert has struggled all season, despite some moments where he showed real NFL skills. Why did the coaching staff wait five games to bench him?

Kaepernick was recovering from injury, sure, but he was healthy enough to play in the preseason. Chip shot down the idea of being worried about new damage triggering the injury-only guarantee in Kap’s contract, noting that he played him at the end of the Rams game and kept him active as the backup QB. (The Niners have tons of extra salary cap room, and money is Trent Baalke’s problem, not Chip’s.)

No one knows for sure, but Chip’s go-slow approach fits his long-standing football philosophy. He’s a process guy. In other words, doing things the right way is as important as knowing the right things to do. No shortcuts, lots of practice.

You’ve probably noticed how often he tells reporters not to overthink or overanalyze things. (He did it again Thursday, when asked why he announced Kap was starting so early in the week.)

That’s especially true for players. The game moves too fast to be puzzling out your next step. You need to react based on well-honed instinct, which requires lots of practice repetitions after you’ve fully understood the system.

This is especially true for quarterbacks, who are processing a huge amount of information while (hopefully) making their key decision on each play in less than two and a half seconds. Oh, and try not to let all those 280-pound world-class athletes who are trying to crush you be a distraction.

Let’s face it, Kaepernick’s career has not gone super well the last couple of years, and confidence matters. Kelly is attempting a major reclamation project here with a talented, flawed QB. Throwing him into the grinder before he or the rest of the team was ready would have made failure very likely.

Several things had to happen for Colin Kaepernick before he was ready to play.

1. He had to be fully recovered from his injuries.

This involves more than the healing of surgical scars and torn ligaments. Last year I interviewed Bill Knowles, the sports science guru who led Sam Bradford’s recovery from two consecutive ACL tears, for my book “Controlled Chaos.” He follows the reconditioning approach, which Chip Kelly adopted in Philadelphia.

Reconditioning says that you can’t just repair an injured body part in isolation, and pick up where you left off the day before the damage. Knowles told me that

… a serious joint/tendon/muscle injury should be looked upon as a neurophysiologic dysfunction, not just a basic peripheral musculoskeletal injury. With this in mind we must train movements, not muscles, during all stages of post-injury care.

In other words, it’s the brain-muscle connection that needs to be repaired, not just the muscle.

Knowles also told me that reconditioning is an excellent time to correct a player’s mechanics -- but only if you use a team approach with the position coach and strength/conditioning team, since rehab trainers are usually not well versed in the specific skills for a sport.

Injury is an opportunity. If you get hurt, the opportunity to rebuild the athlete from the ground up does indeed exist.

As he noted though, that approach takes more time. You have to build a player’s movements and reflexes up from scratch.

2. Kap had to learn and practice the system.

That requires film and classroom study followed by lots of snaps. But with Gabbert starting, the 49ers couldn’t neglect the practice snaps of their actual starter while they brought the injured guy up to speed.

Kelly praised Kap’s classroom understanding and work ethic. But there is just no substitute for the muscle memory you get while actually running the plays. Chip:

“If your players have not run that [game-deciding play] over a thousand times in practice, you will not have a chance to be successful. … My old high school coach told me a long time ago that ‘If your head is moving, your feet are not.’ That means if you are thinking about what to do, you are not doing it as fast.”

3. Chip needed to win Kap’s trust.

As Kelly unpacked his boxes in Santa Clara last January, Kapernick was done with the Niners, and Trent Baalke in particular. He spent the off-season trying to get out of town. His new coach has spent months carefully building an independent and more positive relationship with the quarterback, which was essential to have any hope he could be the team’s starting quarterback again.

Now Kap has a new contract which gives him the right to bail out on the Niners at the end of the season. One possibility is that Kap hopes just to play well, go free agent and make some coin. But another is that he fits in with the team, clicks with his new coach and the offense, and decides to stay. In that case, replacing Baalke might be part of the negotiations, something the Niners are probably thinking about already.

4. The team needed to learn the new scheme.

With a major offensive change, a rebuilding OL and a serious shortage of receiving talent, it was inevitable that things would be rough for the first few games. It made no sense to try to rebuild a QB in those first few games.

5. Chip needed to tweak his system for Kaepernick.

We’ve already seen a lot of new wrinkles in Kelly’s offense. But he didn’t know how Kap would fit into his scheme until he could see him actually run it in practice. Now that he is getting some real-time, on the ground data, he’ll adjust the plays to Kap’s skill set.

What exactly that will look like is anybody’s guess, but clearly Kaepernick has a better arm and is more willing to take shots downfield. That should open up the run game and stretch secondaries vertically.

Several writers predicted a quarterback switch around this time of the season, but I don’t think it’s fair to say that Kelly planned this switch all along, or that the first five games were a sort of pre-season that unfortunately counted in the standings.

Given the way Kelly likes to run his teams, Colin Kaepernick was nowhere near ready to start before now, and his potential is too large to bring him back before he’s ready. I think that from Chip’s perspective, Kap wasn’t really a choice before now, and Gabbert — the incumbent starter — deserved every chance to show he could lead this team.

Well, he got that chance and it didn’t work out. Now Kap has had plenty of time to round into shape and it’s his turn. There’s no guarantee he’ll be any better, but Kap has raw skills and a proven ability to take this team deep into the playoffs.

Kelly knows very well how hard decent quarterbacks are to obtain in the NFL. He’s never had one, but managed to make Nick Foles a stud for most of a season, and rebuilt Sam Bradford from an injury tragedy into a winning game manager. This season was always going to be a tough slog for the Niners, but they’re on the way to decisively determining whether either of their existing QBs can ever work.

And if both flop, the team should be in great position to draft a possible franchise quarterback next spring.