It ain’t about a spy as we’ve been hearing all week. No one has solved the read option yet. Colin Kaepernick just isn’t playing well.

Kaepernick is supremely talented, both throwing the ball and running. But he’s raw. To date, he’s shown little ability to hang in the pocket and read through his progressions. Against the Seahawks and Colts, when his first receiver wasn’t open, he was ineffective entirely. Kaepernick often stays on his receiver too long, not recognizing the fact that the coverage or defender’s position dictates that his receiver won’t be open. He’s been late moving to his 2^nd read as a result. Sometimes he doesn’t even get to that 2^nd read, instead fleeing the pocket and leaving several big plays on the field.

Where the spy comes in is on these scrambles. It’s not even necessarily the spy itself that has limited Kaepernick’s scrambling ability. Defenses are more aware, their senses heightened over the threat of Kaepernick’s running ability. As a result, teams are rallying to him when he scrambles, quickly reacting to him, preventing the big run.

But the Niners’ offensive woes really go back to Kaepernick’s inability to succeed from the pocket. He’s an imprecise quarterback, so far incapable of getting to his 2^nd, 3^rd, and 4^th read.

To be fair, his receivers haven’t helped. For two straight weeks they’ve been shut down by man coverage, creating very little separation. Most surprisingly, free agent acquisition Anquan Boldin was physically dominated by Richard Sherman in their Week 2 matchup against Seattle. This didn’t help Kaepernick’s cause.

Only the most precise quarterbacks can succeed against tight coverage by throwing receivers open and putting the ball on the money with great anticipation and timing. Kaepernick hasn’t been able to do that consistently thus far in his career, and as talented as he may be, consistency is the name of the game for quarterbacks in the NFL.

When the 49ers offense took off in 2012, it was because of the read option. The play put defenses in conflict. It made normally aggressive teams passive, making Kaepernick’s job that much easier. The riding action put defenders in conflict, especially linebackers and safeties. Their indecision allowed blockers to get to the second level consistently in the run game. When defenders attacked the run, it created huge throwing lanes and wide-open receivers in the middle of the field.

Michael Crabtree and Vernon Davis had the ability to get open on their own a year ago, but the biggest reason for their success was the wide open throwing lanes created by linebackers and safeties who vacated their zones reacting to the read option.

This year, the read option has been almost absent from the 49ers offense. Kaepernick has only run the ball 14 times on the read option through 3 games. The offense has suddenly become a pass-first scheme. Frank Gore has every right to be mad.

Unfortunately for the 49ers, Kaepernick is not the type of quarterback who can drop back every play and pick apart a defense from the pocket a la Peyton Manning. The threat of his legs sets everything up in the passing game, and the 49ers have gotten away from that.

The read option and the running game in general have been sporadic elements of the offense this season instead of staples. Colin Kaepernick is only 13 starts into his young career, and he has a bright future because of his physical gifts. Yet until he can harness his raw talent, he needs help. He needs help from the threat of his own legs as well as an established running game. This was the formula that dominated in the playoffs a year ago. It needs to resurface if the 49ers want to regain that spark that sent them to Super Bowl XLVII.