I posted this in a comment earlier this morning, but I figured I'd post it here so that more people can see it:

It's something I've noticed more as of late with Crabtree back, but Kaepernick is quite good on 3rd down. By DVOA, the 49ers have the best passing offense on 3rd down. In this game, Kap was only 3 of 7 for 37 yards (and 2 rushing first downs), but that's kind of expected against a defense like this, especially with many of the 3rd downs being 3rd and long. The 2 rushing first downs were the QB sneaks on 3rd and 1. Not to mention, he only threw the ball 4 times in the 2nd half. These are Kap's passing numbers by down this season:

This is also impressive given that only 11 of those attempts on 3rd down are on 3rd and short (1 or 2 yards). It's not a huge sample, but when it's 3rd down and they're forced to pass, Kaepernick has been getting it done, without any kind of play action being usable. Being this team uses 22 personnel more than any team and were with only 1 reliable WR earlier in the season, his numbers on 1st and 2nd down make sense. It's hard to have success and gain yards when you have one option that's a WR. This is why I get frustrated with Roman. While it's been better as of late, mixing up the personnel on earlier downs would be nice, because Kaepernick has proven that he excels a lot more in these non-running formations. He had 136 attempts with 3 WRs, and had an 8.27 YPA and completed 61% of his passes.

An example of why success on 3rd down (besides the obvious) is crucial is RG3 this year. Last year, his numbers were horrific on 3rd down, but he managed to have a ton of success on 1st and 2nd due to the play action and offense he was playing in. It was basically the Baylor offense with some west coast elements:

Teams adjusted. RG3's numbers are about as bad on 3rd down, but he didn't have the success on 1st/2nd that he did last year because the stuff they used last year (basically training wheels) didn't work, or was taken out in anticipation of not working. Part of his struggles were from not being fully healthy, but he just struggled as a passer.

In relation to this upcoming game, I've always maintained that a ton of Russell Wilson's success was the result of the other 10 guys on offense. He's a good player, but in watching their games where he succeeded, I'm not sure I've ever seen so many wide open receivers. Like, guys with no defender within 10 yards. By my quick research, he has the highest YPA in the league on 1st/2nd down. When 3rd down comes and the play action is no longer working, the results aren't as good, although not bad:

In the past 6 games or so when Wilson has been struggling, it's been apparent that he's receivers are failing to get the separation they did throughout the season, and teams are adjusting their strategy. Instead of crashing hard and trying to get quick pressure, teams are doing everything they can to contain Wilson, even if it means more time to throw. They're keeping him in the pocket and forcing him to find the passing lane. It was blown off for the last 2 years, but you have to think the height is coming into play. That's not all of it, but it's a part. Another part is just inaccuracy and poor decision making, for whatever reason. This is relevant to this post because while he's doing about the same on 3rd down, the early success on 1st and 2nd isn't there. It would be a stretch to saying he's playing bad, but more appropriate to say the help he was getting to get those gaudy numbers isn't there nearly as much. When he's forced to do it himself, you get the 3rd down numbers.

Two other notable QB's for comparisons sake:

Aaron Rodgers in 2012 (last full season)

Drew Brees in 2013

While I'm not explaining anything new or revolutionary, you can see the main component of their success is having success on 3rd down, generally when teams aren't worried about the run or going to bite on the play action. Their completion percentages are worse, but that's to be expected. The key figure is the YPA.

I made this post as a comparison, and as a way to illustrate how good Kaepernick has been on 3rd downs. Both Wilson and Kaepernick have about 30% of their runs going for first downs, but it's a lot harder to do that against a great defense. No team wants to get into 3rd down (and long), but for this upcoming game, it's hard to deny which QB has been better when his team puts him in a tough spot.