Jim Harbaugh has found himself in the best, but possibly also the worst, situation for his team.

I mean, what coach doesn’t want the choice between two talented and more than capable quarterbacks? Nothing is worse than lacking a capable quarterback. So, having two must be a fantastic scenario. The only problem is that some serious complications could rise from the fallen’s ashes.

Alex Smith led the 49ers to within minutes of a Super Bowl berth a season ago and looked to have them on the brink of another deep playoff run this season. He’s been the most accurate quarterback in football this season, completing 70 percent of his passes and throwing 13 touchdowns to just five interceptions, which is a better rate than every other quarterback besides Tom Brady (24 and three), Robert Griffin III (16 and four) and Ben Roethlisberger (17 and four).

So, Smith would be starting on roughly three-quarters of the teams around the league right now. Yet his own backup might have just sniped his job away, a la Brady and Drew Bledsoe circa 2001.

Now, I’m not directly comparing Colin Kaepernick to Brady. Let’s get that straight right out of the gate. I mean, facts are facts — one guy has started two NFL games, and the other guy has won three Super Bowls and two MVP awards. The credentials don’t exactly stack up evenly — at least not yet.

But in the same way Brady usurped Bledsoe a little over a decade ago, Kaepernick seems to have seized a similar opportunity in San Francisco. The 49ers and 2001 Patriots both boasted staunch defenses that were among the best in points against (49ers rank first, ’01 Patriots were sixth) as well as in total yards (49ers are second, ’01 Patriots were eighth).

That stingy defense provided Brady with some leeway to build confidence and the opportunity to learn from his mistakes on the way to the playoffs. Kaepernick doesn’t have as much time to learn, but he’s also dealing with a superior defense and much more athleticism than Brady was blessed with — er, without.

Through three games as the primary quarterback under center, Kaepernick has been nearly as accurate as Smith, completing 66 percent of his passes. He’s also been just as productive, if not more, scoring five touchdowns, including two on the ground, and throwing just one interception.

The production is clearly there from Kaepernick. He has maintained his accuracy, even through the switch. And although he doesn’t have the playoff experience of Smith, given last postseason, Kaepernick is also the 49ers’ best option to actually win the Super Bowl — again, a la Brady.

Kaepernick has the type of athleticism and speed that forces opposing defenses to adjust their game plans. But he also boasts one of the strongest arms in football, which also gives him an edge over Smith. The combination has proven deadly in his first few games behind center and might even make 49ers fans reminiscent of the legendary Steve Young.

Such early comparisons to the likes of Brady or Young are somewhat cruel and unfair, but parallels do exist. Kaepernick is taking over for a very capable and impressive quarterback in the middle of the season, just like Brady nearly a decade ago. And although the two may not have all that much more in common — maybe only their Bay Area roots — the comparison can certainly be made.

Now, with maybe the best defense in football behind him and an offense that just continues to find ways to produce each week, Kaepernick is in good position to lead the 49ers to the Super Bowl for the first time in nearly 20 years (1994). And just as Brady was for the Patriots more than a decade ago, Kaepernick is the 49ers’ best chance of not only reaching that lofty game but also winning it.

Have a question for Luke Hughes? Send it to him via Twitter at @LukeFHughes or send it here.

Pick Six
The six biggest movers of the past week in the NFL

1. Ray Rice, RB, Ravens — UP: Rice proved Sunday that he’s the best 4th-and-29 back in the NFL, not to be confused with Freddie Mitchell, who is still the best 4th-and-26 receiver ever. A big play for a little man, and the Ravens aren’t backing down for anybody.

2. Fireman Ed — DOWN: His Jets roots are stronger than an oak tree, but even those wither away eventually. Fireman Ed had a great run as the Jets unofficial mascot, but now his run is over, and Gang Green can look elsewhere for their hopeless motivation.

3. Robert Griffin III, QB, Redskins — UP: I find it difficult to say anything bad about this kid. He follows up a one-incompletion performance by threading 20 of 28 for 300-plus yards and four scores less than a week later, on Thanksgiving no less. RG3 is the real deal. The Cowboys, on the other hand, are not.

4. Adrian Peterson, RB, Vikings  — DOWN: Peterson needed to hail a taxi to get to the stadium Sunday. And after fumbling twice in a 28-10 blowout in Chicago, I’m surprised coach Leslie Frazier didn’t make him take another one back to Minneapolis.

5. Jim Schwartz, head coach, Lions — DOWN: Know the rules, Jim. And if you’re not so sure of yourself, then maybe don’t chide other coaches about their own misgivings. Glass houses, Jim. You don’t throw challenge flags in glass houses. Or something like that.

6. PED Policy — DOWN: If Brandon Browner and Richard Sherman are indeed found guilty in their PED appeals, then that will make eight players suspended for violating the league policy since Sept. 1, 2012, including five in the past month. And because the NFL is unable to release information on the testing, the Adderall excuse is suddenly all the rage among players. Either go get a prescription, admit to you’re a fraud or let’s get the NFLPA to change this hush-hush policy.