Is Kyle Shanahan’s offense still working?

This has been a rough year for the Faithful, between injuries, close losses and the underwhelming development of several highly-touted young players on the San Francisco 49ers roster.

Most see these problems as temporary, with the combination of Kyle Shanahan’s offensive schemes, Jimmy Garoppolo’s arm, and a high draft slot for GM John Lynch combining to paint a bright future.

Is it time to question that future, though? The 49ers have struggled offensively this year, scoring under 20 points in four of the last six games. Could it be that Kyle Shanahan’s offense is not as great as everyone hoped it would be? Offensive wizards can get figured out in this league (just ask Chip Kelly).

Let’s start by acknowledging what we don’t know — the exact plays, reads and defensive coverages on each play. Deception is a big part of the battle between offensive and defensive coordinators, and unless you wiretapped the helmet mics during the game, none of us really know what the calls were.

That said, Shanahan’s offense is pretty simple in some ways — a lot of outside zone runs mixed with play action. While he’s innovative in moving skill players around his formations and good at getting production from all of them — including his fullback — Shanny’s scheme is more multiple than tricky.

This should keep him relatively immune from being “figured out” in general terms, but it moves the battle against defensive coordinators into individual game plans and player matchups. The commonly used metaphor of football as a chess game doesn’t really work, because talent changes everything. In football, one “knight” might be able to move three squares down and three over; another could go four down but can’t cut to the right.

The problem is that injuries and a general shortage of talent have left Shanahan with little to work with. We can’t really tell if a play is creating lots of possibilities, when the surviving players aren’t capable of executing it. The loss of Marquise Goodwin in particular has been a huge issue, allowing defenses to collapse and removing Shanahan’s deep shots from his arsenal. Pierre Garçon’s injuries have compounded the problem.

Matt Breida, Nick Mullens, and Jeff Wilson, Jr. have overachieved beyond anyone’s wildest dreams, which is a great sign of the power of Shanahan’s scheme (and Bobby Turner’s coaching of the running backs). But there are reasons why each was a UDFA, and in general any DC would rather game plan against them than Garoppolo, Goodwin, and Jerick McKinnon.

If you look at production during games, there are encouraging signs. Even with all of their problems, the 49ers are 15th in the league in offensive yards per game (363.3), and 7th in running yards (129.2). However, they are 21st in point per game (21.3), which points both to turnover problems and red zone weakness. The very young skill players, with less experience against top-level competition, are vulnerable on both scores.

What we are not seeing is some kind of schematic adjustment that undermines the advantage of Shanahan’s scheme, the way that, say, scrape exchanges countered read-option run plays. When the offense stalls, it’s the result of errant passes, illegal motion and holding penalties, or sacks.

Tampa Bay threw a lot of pressure at Mullens, and his greenness showed. He felt the pressure and couldn’t get the ball to open receivers in many cases. It’s worth noting that Tampa Bay’s offensive coordinator, Todd Monken, was Mullens’ coach at Southern Mississippi. So they had extra insight in the rookie QB’s vulnerabilities.

Against Seattle, Shanahan dialed up a lot of screen passes, which were effective in helping Mullens handle the predictable pressure. This hasn’t been a big part of Shanny’s scheme, even though opposing coaches such as Andy Reid have been torturing this team with screens all year.

Shanahan, in my opinion, prefers taking shots downfield or between the numbers in these situations, to move the ball downfield more aggressively, but he’s limited by wide receiver injuries, and doesn’t have a quarterback capable of finding the receivers he has. This was a necessary adjustment, but I don’t think we’d see that with healthy starters.

We won’t know for sure if Shanahan is less than his reputation would suggest until next year, with a talent infusion and healthier players. It’s the job of coaches to make the most of what they have, but Shanahan is facing extreme limits.

It’s possible he’s a guy who needs top level talent (say, Matty Ice and Julio Jones) to really do well. But I think 49ers fans would prefer that to a coach who specializes in getting more than you’d expect out of a bunch of bad players. Jed York and the 49ers front office show every sign of wanting to get back to the Super Bowl and having a pretty good plan for getting there. It just might take a bit longer than we hoped.