SAN FRANCISCO -- Let's start with praise for Colin Kaepernick. It is a pleasure to watch him work. It really is.

On Sunday, he put away the Miami Dolphins with a 50-yard run that was more of a prance, Kaepernick on his own, the overmatched Dolphins staring at him, knowing they had no chance to stop him. Touchdown.

The 49ers' quarterback controversy is so passe, so old. Jim Harbaugh made the correct decision going with Kaepernick over Alex Smith. If you have any lingering bitterness, please put it to rest.

And think about this. It always is important to praise the team that wins a game in the NFL, games being hard to win even against losers like the Dolphins. So, all praise to the Niners for beating Miami 27-13.

Now, let's talk some serious football. Although the 49ers no longer have a problem at quarterback — and they don't — they do have other problems, serious problems. These problems proved, well, problematic against Miami, and in the interest of honesty and full disclosure, it's important to examine them with open eyes.

The 49ers' offensive line gives up a lot of sacks. It gave them up when Smith was the quarterback, and it gives them up now that Kaepernick is the quarterback.

Anthony Davis allowed three sacks — count them — in the first half. He got buried by Cameron Wake on several occasions. In all, Kaepernick got sacked four times — you could look it up. He also got hit so many times you wonder if he moonlights as a sparring partner for Juan Manuel Marquez.

Here's how sackage works on the Niners. The offensive linemen are big and slow — the exact opposite of what Bill Walsh advocated.

They run block exceptionally well. Think of snow plows clearing a street.

And they pass block well on play-action passes — fake the run and pass the ball. But for play action to work, the run game has to go gangbusters.

If the Niners' run game isn't gangbusters, teams don't go for the play-action fake and Kaepernick has to pass, and the line doesn't hold. (I was tempted to write "the center cannot hold," but I don't think Yeats — you remember old Billy Yeats? — had that kind of center in mind.)

Sacks were not a devastating problem against the thoroughly beatable Dolphins, although the 49ers had trouble beating the thoroughly beatable Dolphins. It certainly could be a problem next week in New England — I'll get back to the Patriots game in a moment.

And sacks could be a problem in Seattle. And they sure could be a problem in the playoffs. Teams that aspire to the Super Bowl usually pass with less all-out anxiety than the Niners.

There is another problem and this one also persists post-Alex. The 49ers are dreadful on third down. Against Miami, they converted two of 10 third downs which, as any fifth-grade kid knows, comes to 20 percent. Even the Dolphins did better, 38 percent. It is no stretch to say the Niners need to improve on third down, although time is running short.

If the third-down problem was there with Smith and is still there with Kaepernick, where does it come from?

It probably doesn't come from the quarterback. It almost surely comes from above the quarterback. I'm taking a leap here, but I think it comes from the offensive coordinator, Greg Roman. He calls all the plays but is allowed to draw up only run plays. Other coaches create the pass plays and red zone plays. Have you ever in your life heard of an arrangement like that one?

After the game, Harbaugh said of Roman,"I thought Greg called a great game. He always does."

Roman sure called his usual game, but do you call that great? The 49ers scored six points in the first half. That's Alex Smith territory. The only reason they took a 13-3 lead early in the third quarter was because some confused Dolphin tried to catch a punt at his 9-yard-line when he should have let it bounce.

Naturally, he fumbled the punt and the Niners recovered the ball and quickly scored a touchdown. That play by the Dolphins shows why they are a bad team.

Even so, it still was a game late in the fourth quarter when Kaepernick performed his prancing run. If you're keeping count, Roman needed a recovered fumble and a heroic play by Kaepernick to score two of the Niners' three touchdowns.

This is not a good offensive formula game after game, and it makes you wonder about next week in Foxboro. With protection issues and a paucity of third-down conversions, it will be hard for the Niners to beat New England. The Patriots score a lot, and the 49ers will have trouble keeping pace because they don't keep drives alive and, as noted earlier, they don't pass protect well when they absolutely must throw.

I didn't mean to make you sad, angry or disgruntled by what I just wrote. I praise the 49ers for defeating Miami.

For more on the world of sports in general and the Bay Area in particular, go to the Cohn Zohn at cohn.blogs.pressdemocrat.com. You can reach Staff Columnist Lowell Cohn at lowell.cohn@pressdemocrat.com.