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San Francisco 49ers quarterback Colin Kaepernick (7) leaves the field after pre-game game warm ups against the Indianapolis Colts at Candlestick Park in San Francisco, Calif., on Sunday, Sept. 22, 2013. (Josie Lepe/Bay Area News Group)

SANTA CLARA -- It all happened so fast, and so easily, once Alex Smith was moved aside last season and Colin Kaepernick took control of the 49ers offense.

The 49ers went from nice and steady to light-speed, just like that. No hiccups, no slowing down.

Until the past two Sundays, that is, when the 49ers and Kaepernick suddenly started to experience the residual effects of that quantum jump.

"You know, football is not easy," coach Jim Harbaugh said Monday, less than 24 hours after the 49ers' dismal 27-7 loss to the Indianapolis Colts. "There are struggles. And it's one of the things you enjoy about the game, that there are struggles.

San Francisco 49ers Colin Kaepernick (7)  leaves the field  in the last 30 seconds as they are losing 27-7 against Indianapolis Colts in the fourth quarter
San Francisco 49ers Colin Kaepernick (7) leaves the field in the last 30 seconds as they are losing 27-7 against Indianapolis Colts in the fourth quarter at Candlestick Park in San Francisco, Calif., on Sunday, Sept. 22, 2013. (Josie Lepe/Bay Area News Group)

"We've got some adversity, there's no question about it. And we also have the rare opportunity of staring adversity in the face and whipping it."

Of course, the 49ers have to deal with the indefinite loss of linebacker Aldon Smith -- their 2012 team MVP -- as he enters a substance-abuse treatment program.

And they have to deal with their first dip under .500 and their first losing streak since Harbaugh arrived.

But the broadest 49ers struggle is the one occurring on offense. The simple fact is that the 49ers under Kaepernick are far more reliant on their quarterback than they ever were under Smith.

When Kaepernick has been hot in his 13 NFL starts, the 49ers have won big, against any kind of defense, and that is why they picked him over Smith.

But when Kaepernick has been off rhythm, or when opposing defenses have taken away his favorite things, the 49ers have had trouble figuring out what else to do.

Meanwhile, the coaches seem to be bending their plan specifically to keep Kaepernick healthy -- he barely played in the preseason, and now even in the regular season they have encouraged him to stay away from large downfield hits.

Why? Because the man backing up Kaepernick is Colt McCoy, so the 49ers are doing everything to keep Kaepernick healthy.

All of this redirected focuses changes a team. It doesn't mean the switch from Smith was wrong. Kaepernick is the superior quarterback, far superior athlete, superior thrower, and he projects to superstardom.

But the adjustment is still happening, not always perfectly.

In the 49ers' five games before the Seattle debacle, including three playoff games last season, the Kaepernick offense generated 33 points per contest and an average of 464.2 yards.

In back-to-back losses to Seattle on Sept. 15 and the Colts on Sunday, the 49ers offense has managed only 10 total points, committed seven turnovers and averaged only 230.5 yards.

Even when the 49ers look as though they're going to run the ball well -- as they started to Sunday -- they always seem to revert to putting it all on Kaepernick.

The point is, the 49ers were far less dynamic with Smith at the helm, but they were probably more consistent.

In the past two weeks, Kaepernick has put up passer ratings of 20.1 and 49.9 and the 49ers have scored only 44 points, second fewest in the NFC.

Defenses are taking away the read option explosion plays and are corralling Kaepernick in the pocket when he drops back, and Kaepernick looks frustrated by the development.

"They put a spy on me," Kaepernick said Sunday of the Colts defense. "So, I mean, they have one more to account for me. I have to be able to make throws down the field."

What do you do with a quarterback who can do almost anything? Sometimes you come up with all the exotic stuff and you forget about the basic things.

With Smith, that was never a problem, because the 49ers coaches were limited to a nice, tight package -- run the ball to set up the pass, pass the ball only in the safest windows, and they knew Smith could do that.

It was predictable and potentially very beatable against physical defenses, but it was consistent. It was the 49ers' identity.

Now they are all over the map and totally disconnected from their 2011 power game. It is all about No. 7, rise or fall.

Kaepernick can throw a beautiful deep ball, but he needs receivers who can get deep, which the 49ers do not have at this time, especially without tight end Vernon Davis, who missed Sunday's game and is a question mark for Thursday at St. Louis, and Michael Crabtree, who is out at least for a few more weeks.

Meanwhile, Smith has led Kansas City to a 3-0 record, playing it safe and sane, and the Chiefs have yet to commit a turnover.

The Chiefs are playing the way the 49ers used to -- power, safety, efficiency. Which is what the 49ers ditched when they went with the supersonic quarterback last season.

It was a bold call then, it was the right one, and the 49ers offense went hyper-speed for a while.

But it is experiencing hiccups now, because football just isn't meant to be that easy. Now we will see how Kaepernick and Co. figure it all out.

Read Tim Kawakami's Talking Points blog at blogs.mercurynews.com/kawakami. Contact him at tkawakami@mercurynews.com.