Jeff Chiu/APGiants left-hander Madison Bumgarner is a big reason the Giants have the best record in baseball.

Jeff Chiu/APGiants left-hander Madison Bumgarner is a big reason the Giants have the best record in baseball.

Decision to go with Kaepernick over Smith coming back to haunt 49ers

Jim Harbaugh picked the wrong quarterback last year and that decision is going to cost the 49ers another shot at the Super Bowl.

You remember how it went last year: Alex Smith, having his best season, suffered a concussion and had to sit out a game. That gave Harbaugh a chance to test out his new toy, Colin Kaepernick. He stayed with Kaepernick the rest of the way.

Despite his disappointment, Smith helped Kaepernick with advice on the sidelines during the games. Kaepernick made spectacular plays, more often with his legs than his arm, and the Niners got to the Super Bowl.

This year has gone much differently for Kaepernick and Smith. After a big season-opening game when he threw for more than 400 yards against the Green Bay Packers, Kaepernick has been stymied by teams with good defenses. He still looks good against teams like the Jacksonville Jaguars, winless when they played the 49ers, but defensive coordinators for good teams have figured out how to stop him.

On Sunday against the Carolina Panthers, he looked totally bewildered, throwing for just 91 yards and being sacked six times for 45 yards lost. Not coincidentally, the 49ers couldn’t score a touchdown in a 10-9 loss.

Meanwhile, Smith has quarterbacked the Kansas City Chiefs to a 9-0 mark, though that spotless record is in danger with two games in the next three weeks against the Denver Broncos.

Many in the media scorn Smith as a “game manager.” Excuse me, but isn’t that what a quarterback is supposed to do? What they mean is that Smith doesn’t often throw deep passes, though he certainly proved he could do that when necessary in a dramatic fourth-quarter comeback against the New Orleans Saints in the 2012 playoffs.

No writer or broadcaster who knows anything of 49ers history should make that mistake. How many long passes did Joe Montana throw? Bill Walsh’s offense was based on “moving the chains,” with short passes to receivers who were expected to run for longer gains after the catch. The extreme example was John Taylor’s 92- and 96-yard touchdowns in a game against the Rams.

The short-pass, moving-the-chains offense also helped the 49ers’ defense by keeping them off the field for long periods. That’s exactly the way it’s working with the Chiefs now.

Meanwhile, Harbaugh and the 49ers are stuck. Whether he’s working out of the shotgun or taking a regular snap from center, Kaepernick has struggled against good defenses. When ESPN NFL analyst Trent Dilfer criticized Kaepernick for not going through his progessions, Kaepernick made a smart-aleck remark about Dilfer not knowing his progressions. He didn’t have to. When Kaepernick only looks at one receiver, his usual pattern, it’s obvious what’s happening. Or not.

The game in New Orleans on Sunday is a critical one for the 49ers because another loss could put them three games behind the Seattle Seahawks and probably in a tie with the Arizona Cardinals, who face the toothless Jaguars.

My advice to Harbaugh: Run Frank Gore until he drops to keep the ball out of the hands of Drew Brees. He can’t rely on his own quarterback.

Glenn Dickey has been covering Bay Area sports since 1963 and also writes on www.GlennDickey.com. Email him at glenndickey36@gmail.com.Colin KaepernickGlenn Dickey

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