Since one of these two guys will most likely be starting for us at QB next season let's look at their career numbers. One of these two guys has clearly been the better QB in the NFL.
The only area in standard passing metrics where Sanchez is superior is sack rate. Sanchez played behind some really good offensive lines early in his career in NY. In every other stat Colin Kaepernick is better and in some cases significantly better. To show up on the all-time passing lists you have to have a minimum of 1500 passing attempts. Kaep does not have that yet, but if he had, he would be tied for 2nd all-time in lowest interception % (tied with Russell Wilson). Only Aaron Rodgers has a better career int% (minimum 1500 attempts) at 1.6%.
If we look at the advanced passing metrics (everything scaled to 100), here is the comparison of the two.
This backs up what we saw in the previous chart, but it also show that Kaep has been average to above average in most metrics through his career while Sanchez has generally been below average. Remember 100 is the NFL average in this chart.
Here's where it gets really interesting. Let's compare their passing performance in the playoffs.
Both QBs played well enough for their teams to go 4-2 during their two years in the playoffs. Sanchez actually outplayed Kaep in the playoffs in many stats. I find it interesting how close the two are in terms of playoff experience and stats. Sanchez has one more completion on five fewer throws. They both have two 4th quarter comebacks and two game winning drives in the playoffs. The most critical stat is that Sanchez dramatically improved his TD:INT ratio in the playoffs while Kaep's got worse. Both QBs had very good offensive lines during their playoff runs and both teams had above average rushing attacks.
Mark Sanchez has never been nor will he ever be the runner that Colin Kaepernick is, but we should at least look at their rushing stats.
For his career Sanchez has actually been decently effective at scoring on QB sneaks. His 13 rushing TDs in 75 career games (one every six games) is better than T*m Br*dy (one every 13 games) and Ben Roethlisberger (one every 11 games) and comparable to John Elway (one every seven games). That being said, Kaepernick is a genuine threat with his legs.
Kaep, unlike Sanchez, used his legs to great effect in the playoffs. Sanchez has 11 carries for 9 yards in the playoffs. Kaep has 51 carries for 507 yards and 4 TDs in the playoffs.
In terms of holding onto the ball, Sanchez has 51 career fumbles in 75 games (one fumble every 1.5 games) while Kaep has 31 fumbles in 57 career games (one fumble every 1.8 games). Despite running with the football on a regular basis, Kaep does not (butt) fumble as often as Sanchez. For comparison, Peyton Manning only fumbled once every 3.5 games during his career. Eleven of Peyton's 77 career fumbles occurred in 2013.
So I've done the analysis. I still would prefer to have Kaepernick as our starting QB for 2016, but I'm less worried about going into the 2016 season with Sanchez having a possibility to be the starter now than I was before I wrote this. In all honesty, I think Sanchez can be an upgrade to the level of QB play that we had in Denver last season (that's not saying much) if he ends up as our starter.