Quarterback Controversy in San Francisco

Despite their 5-2 record so far, the San Francisco 49ers have a problem, and though it is not a new one it still may come as a bit of a surprise. The problem is Alex Smith, and more specifically, his psyche.

After San Francisco’s dalliance with Peyton Manning and the Peyton Manning Sweepstakes this past offseason, there was a dicey period during which relations between Smith, coach Jim Harbaugh and the 49ers’ brass were understandably tense. When you have had the sort of rocky tenure with a club that Smith has, and then you deliver what you think is the season that will finally get everyone off your back only to discover that your team is still looking elsewhere for help, that is bound to play with your head. It is hard to be confident when your employer does not demonstrate confidence in you.

Fast-forward to this season. After he finally agreed to a three-year, $24 million deal with San Francisco and started the year by leading the 49ers to impressive wins over the Green Bay Packers and Detroit Lions, the team hit a speed bump against the Minnesota Vikings in Week 3.

Once Week 4 came along, Harbaugh started inserting Colin Kaepernick into the offense here and there. To the casual observer it might not seem like this is a big deal. However, for a quarterback whose psyche is fragile to begin with, it’s not going to help matters when you are being taken out in games—even if only occasionally—in favor of the second-round pick whom everyone knows is destined to come after you if not replace you outright.

If you take a look at the situations where Kaepernick has been brought in to replace Smith at quarterback, they have almost exclusively been in the red zone, or at the very least when the team is in field goal range. In some of these cases, the moves have backfired, and in others Kaepernick has provided the offense the 49ers needed, but in all of those games—victories against the New York Jets, Buffalo Bills and Seattle Seahawks; a loss in Week 6 to the New York Giants—the message has been clearly sent out to Smith by these moves: We don’t think you can lead us to a score here. Again, how is that supposed to help your team when the supposed leader doesn’t know if or when he’s about to get the hook?

And keep in mind that all of this is taking place despite Smith currently being on pace to meet or exceed almost all of the statistics he accumulated in 2011 (including his interception and sacks totals). Yards passing, touchdowns, completion percentage, quarterback rating; he is improving in all of these categories. This has not escaped Smith’s notice, and while some will attribute his lackluster three-interception performance against the Giants to falling behind early and having to stray from the team’s run-first philosophy in order to try to get the team back in the game, this is actually the return of the old Alex Smith who is trying to do too much on his own. The only reason he feels compelled to do this is because, whether perceived or accurate, he feels he doesn’t have the trust of Coach Harbaugh or the offensive coordinator. And in a sense he is right because the team’s moves support this theory.

Yes, the 49ers managed to pull out a tough one against the Seahawks on a short week and they are heading into their Monday Night Football tilt with the Arizona Cardinals in sole possession of first place, well rested and well prepared for their opponent, but all is not well in 49erville. San Francisco cannot win long-term with this quarterback controversy playing out for all to see. The more Harbaugh plays Kaepernick this season, the more trouble the 49ers are going to be in if they hope to contend for a Super Bowl this season.